4Y7R | pdb_00004y7r

Crystal structure of WDR5 in complex with MYC MbIIIb peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4y7rA1	A: Four-helical up-and-down bundle	X: N-terminal helical domain in restriction-modification system methylation subunit	H: N-terminal helical domain in restriction-modification system methylation subunit	T: Ribosomal_S7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF25175	WDR5 beta-propeller domain (Beta-prop_WDR5)	WDR5 beta-propeller domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	MYC MbIIIb peptide	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein dimerization activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity molecular function activator activity molecular function regulator activity transcription regulator activator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding SCF ubiquitin ligase complex binding DNA-binding transcription factor binding E-box binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of transcription initiation by RNA polymerase II regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process regulation of DNA-templated transcription initiation transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of transcription initiation by RNA polymerase II macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of DNA-templated transcription initiation response to chemical response to xenobiotic stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade regulation of intracellular signal transduction regulation of response to stress intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade negative regulation of signal transduction regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus negative regulation of stress-activated protein kinase signaling cascade MAPK cascade regulation of cell communication negative regulation of MAPK cascade protein-DNA complex organization cellular component organization cellular component disassembly protein-containing complex organization protein-DNA complex disassembly protein-containing complex disassembly cellular component organization or biogenesis positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus response to hypoxia response to oxygen levels response to abiotic stimulus multicellular organismal process cell population proliferation cell activation lymphocyte activation NK T cell proliferation leukocyte proliferation NK T cell activation leukocyte activation T cell activation immune system process alpha-beta T cell proliferation mononuclear cell proliferation lymphocyte proliferation alpha-beta T cell activation T cell proliferation skeletal muscle cell differentiation developmental process cellular developmental process skeletal muscle tissue development animal organ development tissue development striated muscle tissue development muscle structure development skeletal muscle organ development cell differentiation anatomical structure development muscle tissue development muscle organ development striated muscle cell differentiation muscle cell differentiation myotube differentiation positive regulation of DNA-templated transcription positive regulation of miRNA transcription positive regulation of miRNA metabolic process miRNA transcription regulation of miRNA metabolic process miRNA metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of miRNA transcription fibroblast apoptotic process apoptotic process cell death programmed cell death mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process multicellular organism development anatomical structure morphogenesis skeletal system development skeletal system morphogenesis animal organ morphogenesis system development negative regulation of cell population proliferation fibroblast proliferation regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of fibroblast proliferation cellular response to xenobiotic stimulus pigmentation positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization telomere organization positive regulation of telomere maintenance chromosome organization regulation of chromosome organization DNA metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance organelle organization positive regulation of DNA metabolic process regulation of DNA metabolic process myeloid leukocyte differentiation regulation of leukocyte differentiation regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation regulation of cell development regulation of immune system process regulation of multicellular organismal process negative regulation of cell differentiation monocyte differentiation negative regulation of hemopoiesis negative regulation of monocyte differentiation regulation of multicellular organismal development regulation of monocyte differentiation negative regulation of leukocyte differentiation hemopoiesis regulation of myeloid cell differentiation negative regulation of developmental process regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process regulation of hemopoiesis negative regulation of multicellular organismal process leukocyte differentiation mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development renal system development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis nephron development nephron epithelium development ureteric bud development epithelium development tube development mesonephros development morphogenesis of an epithelium tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis kidney development mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium negative regulation of cell division cell division regulation of cell division positive regulation of transcription by RNA polymerase II regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process positive regulation of programmed cell death regulation of B cell apoptotic process positive regulation of lymphocyte apoptotic process leukocyte apoptotic process regulation of apoptotic process B cell apoptotic process regulation of programmed cell death positive regulation of apoptotic process lymphocyte apoptotic process positive regulation of B cell apoptotic process positive regulation of leukocyte apoptotic process regulation of somatic stem cell population maintenance regulation of stem cell population maintenance stem cell population maintenance somatic stem cell population maintenance maintenance of cell number ear morphogenesis embryonic organ morphogenesis middle ear morphogenesis ear development sensory organ development embryonic morphogenesis embryo development sensory organ morphogenesis embryonic organ development negative regulation of gene expression via chromosomal CpG island methylation chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic acinar cell proliferation epithelial cell proliferation negative regulation of programmed cell death negative regulation of apoptotic process ERK1 and ERK2 cascade regulation of cell cycle process regulation of cell cycle positive regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cell communication positive regulation of signal transduction positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator intrinsic apoptotic signaling pathway positive regulation of intracellular signal transduction signal transduction by p53 class mediator apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling positive regulation of mesenchymal cell proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation protein maturation proteolysis protein processing protein metabolic process response to peptide response to interferon-alpha response to cytokine cellular response to cytokine stimulus cellular response to interferon-alpha regulation of kidney development metanephric cap morphogenesis mesenchyme development regulation of metanephric cap mesenchymal cell proliferation kidney mesenchyme development positive regulation of developmental process metanephros development metanephric mesenchyme morphogenesis positive regulation of cell proliferation involved in kidney development mesenchyme morphogenesis metanephric mesenchyme development positive regulation of kidney development cell proliferation involved in kidney development cell proliferation involved in metanephros development metanephric cap development positive regulation of metanephric cap mesenchymal cell proliferation positive regulation of multicellular organismal process metanephric cap mesenchymal cell proliferation involved in metanephros development kidney mesenchyme morphogenesis positive regulation of transcription initiation by RNA polymerase II positive regulation of DNA-templated transcription initiation detection of external stimulus system process nervous system process detection of mechanical stimulus involved in sensory perception of sound response to mechanical stimulus response to external stimulus detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus detection of stimulus involved in sensory perception sensory perception of sound intrinsic apoptotic signaling pathway in response to DNA damage response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation cellular response to abiotic stimulus cellular response to UV response to endogenous stimulus response to growth factor response to nitrogen compound response to alkaloid cell surface receptor signaling pathway Wnt signaling pathway regulation of acinar cell proliferation positive regulation of acinar cell proliferation rRNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II transcription repressor complex protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II transcription repressor complex protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle transcription repressor complex perinuclear region of cytoplasm cytoplasm cytoskeleton spindle microtubule cytoskeleton axon cell projection neuron projection plasma membrane bounded cell projection membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm RNA polymerase II transcription regulator complex Myc-Max complex euchromatin nuclear body
A	WD repeat-containing protein 5	protein binding binding histone binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3Q5ser reader activity molecular adaptor activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity protein binding binding histone binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3Q5ser reader activity molecular adaptor activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K4me1 reader activity	monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process biosynthetic process regulation of gluconeogenesis metabolic process cellular process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process glucose metabolic process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process macromolecule metabolic process developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell division regulation of cell division regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process regulation of transcription by RNA polymerase II cell cycle regulation of cell cycle negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle histone methyltransferase complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen methyltransferase complex nuclear lumen Set1C/COMPASS complex cell projection sperm principal piece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection MLL1/2 complex mitotic spindle cytoskeleton spindle microtubule cytoskeleton MLL3/4 complex NSL complex H4 histone acetyltransferase complex ATAC complex SAGA-type complex MLL1 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR050433	Myc family transcription factors	Family
B	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR002418	Transcription regulator Myc	Family
B	IPR003327	Leucine zipper, Myc	Domain
B	IPR012682	Transcription regulator Myc, N-terminal	Domain
B	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
A	IPR059122	WDR5-like, beta-propeller domain	Domain
A	IPR019775	WD40 repeat, conserved site	Conserved Site
A	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR001680	WD40 repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P01106	cancer Burkitt lymphoma acute myeloid leukemia medulloblastoma myelodysplastic syndrome osteosarcoma glioblastoma cleft palate neuroblastoma hypertrophic cardiomyopathy angiosarcoma ovarian cancer plasma cell myeloma granular cell carcinoma Chromosome Breakage cancer Burkitt lymphoma acute myeloid leukemia medulloblastoma myelodysplastic syndrome osteosarcoma glioblastoma cleft palate neuroblastoma hypertrophic cardiomyopathy angiosarcoma ovarian cancer plasma cell myeloma granular cell carcinoma Chromosome Breakage adult medulloblastoma cutaneous neuroendocrine carcinoma endometrial carcinoma malignant colon neoplasm carcinoma giant cell glioblastoma cervical cancer prostate cancer medullomyoblastoma with myogenic differentiation adenocarcinoma squamous cell carcinoma trabecular adenocarcinoma urinary bladder cancer autosomal dominant polycystic kidney disease gastric cancer primitive neuroectodermal tumor childhood medulloblastoma melanotic medulloblastoma sarcomatoid carcinoma tubular adenocarcinoma liver cancer non-small cell lung carcinoma B-cell chronic lymphocytic leukemia lung disease bone disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia exocrine pancreatic carcinoma breast cancer malignant glioma gastric neoplasm prostate adenocarcinoma hepatocellular carcinoma acute T cell leukemia sinusitis hereditary diffuse gastric adenocarcinoma colonic neoplasm stomach disease intestinal disease large cell medulloblastoma congestive heart failure undifferentiated carcinoma oligodendroglioma urinary bladder neoplasm liver neoplasm atypical teratoid rhabdoid tumor ovarian carcinoma lung benign neoplasm benign colon neoplasm pancreatic intraductal papillary-mucinous carcinoma bone osteosarcoma pancreatic neoplasm breast disease polycystic kidney disease 2 fatty liver disease hematologic disease psoriasis myopathy colorectal cancer invasive ductal breast carcinoma cribriform carcinoma desmoplastic/nodular medulloblastoma ovarian disease lung carcinoma benign neoplasm pancreatic intraductal papillary-mucinous neoplasm lymphatic system disease brain disease pilocytic astrocytoma eye disease malignant ependymoma malignant pancreatic neoplasm prostate disease cleft lip nasopharyngeal carcinoma kidney disease adrenal cortex carcinoma common variable immunodeficiency allergic rhinitis cribriform carcinoma of breast urinary bladder disease liver disease astrocytic tumor uterine disease lung adenocarcinoma ovarian neoplasm endometrial cancer
A	Pharos: P61964	atypical teratoid rhabdoid tumor malignant glioma ovarian cancer glioblastoma medulloblastoma large cell medulloblastoma non-small cell lung carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.