6VGG | pdb_00006vgg

Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth G]	SCOP2B Superfamily	Core binding factor beta, CBF	8042548	3001169	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	p53-like transcription factors	8102164	3000758	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth G]		e6vggG1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (develop294)
D		e6vggD1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (develop294)
A		e6vggA1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F:	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00853	Runt domain (Runt)	Runt domain		Domain
A	PF00178	Ets-domain (Ets)	Ets-domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth G]	Core-binding factor subunit beta	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding DNA binding binding nucleic acid binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation immune system process anatomical structure development leukocyte differentiation RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process definitive hemopoiesis regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process 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 regulation of leukocyte differentiation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation regulation of cell differentiation positive regulation of T cell differentiation positive regulation of CD8-positive, alpha-beta T cell activation regulation of cell development positive regulation of developmental process positive regulation of cell activation multicellular organism development T cell activation positive regulation of leukocyte activation alpha-beta T cell activation regulation of immune system process T cell differentiation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development positive regulation of alpha-beta T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of alpha-beta T cell differentiation regulation of developmental process CD8-positive, alpha-beta T cell differentiation positive regulation of biological process positive regulation of leukocyte cell-cell adhesion regulation of alpha-beta T cell differentiation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion alpha-beta T cell differentiation cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion regulation of cell adhesion positive regulation of CD8-positive, alpha-beta T cell differentiation regulation of T cell activation regulation of CD8-positive, alpha-beta T cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation regulation of CD8-positive, alpha-beta T cell activation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process myeloid cell differentiation anatomical structure maturation cell maturation developmental maturation negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation CD4-positive, alpha-beta T cell activation negative regulation of cell differentiation negative regulation of developmental process negative regulation of cell activation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of immune system process negative regulation of alpha-beta T cell activation	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D	Runt-related transcription factor 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding nucleic acid binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding protein binding bHLH transcription factor binding DNA-binding transcription factor binding protein domain specific binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding chromatin DNA binding	developmental process multicellular organismal process limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development multicellular organism development anatomical structure morphogenesis forelimb morphogenesis appendage morphogenesis anatomical structure development developmental process multicellular organismal process limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development multicellular organism development anatomical structure morphogenesis forelimb morphogenesis appendage morphogenesis anatomical structure development limb morphogenesis ossification bone mineralization animal organ development biomineral tissue development tissue development cellular developmental process connective tissue development cell development skeletal system development cell differentiation chondrocyte differentiation cellular process chondrocyte development cartilage development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process endochondral ossification replacement ossification endochondral bone morphogenesis skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development hemopoiesis regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process T cell differentiation leukocyte differentiation ligamentous ossification positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription response to stimulus response to sodium phosphate response to chemical response to salt regulation of animal organ morphogenesis regulation of odontogenesis of dentin-containing tooth regulation of developmental process regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis regulation of anatomical structure morphogenesis 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 metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process osteoblast differentiation response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus regulation of response to stimulus fibroblast growth factor receptor signaling pathway regulation of cell communication response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway smoothened signaling pathway cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway response to BMP transforming growth factor beta receptor superfamily signaling pathway BMP signaling pathway embryonic organ morphogenesis embryonic cranial skeleton morphogenesis chordate embryonic development embryo development ending in birth or egg hatching cranial skeletal system development embryonic skeletal system development embryonic organ development embryonic skeletal system morphogenesis osteoblast fate commitment cell fate commitment regulation of multicellular organismal process regulation of ossification regulation of cartilage development regulation of chondrocyte differentiation regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal development positive regulation of multicellular organismal process positive regulation of cartilage development positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation nervous system development generation of neurons neurogenesis neuron differentiation negative regulation of signaling negative regulation of cell communication negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction osteoblast development anatomical structure maturation cell maturation developmental maturation intracellular signal transduction SMAD protein signal transduction intracellular signaling cassette regulation of osteoblast differentiation positive regulation of osteoblast differentiation stem cell differentiation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C	DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3')	-	-	-
B	DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3')	-	-	-
A	Transcriptional regulator ERG	DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process cellular developmental process cell differentiation cellular process protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process developmental process cellular developmental process cell differentiation cellular process protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular response to stimulus response to stimulus signaling signal transduction cell communication	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth G]	IPR003417	Core-binding factor, beta subunit	Family
E [auth G]	IPR036552	Core-binding factor, beta subunit superfamily	Homologous Superfamily
D	IPR012346	p53/RUNT-type transcription factor, DNA-binding domain superfamily	Homologous Superfamily
D	IPR013524	Runt domain	Domain
D	IPR016554	Runt-related transcription factor RUNX	Family
D	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
D	IPR000040	Acute myeloid leukemia 1 protein (AML1)/Runt	Family
D	IPR027384	Runx, central domain superfamily	Homologous Superfamily
D	IPR013711	Runx, C-terminal domain	Domain
A	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR000418	Ets domain	Domain
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR046328	ETS family	Family
A	IPR003118	Pointed domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth G]	Pharos: Q13951	acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma medulloblastoma osteosarcoma ulcerative colitis amyotrophic lateral sclerosis cancer Down syndrome IgA glomerulonephritis
D	Pharos: Q13950	cleidocranial dysplasia osteosarcoma rheumatoid arthritis osteoarthritis psoriatic arthritis osteochondrodysplasia Craniofacial Abnormalities uremia metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome non-small cell lung carcinoma osteoarthritis susceptibility 1 adrenoleukodystrophy osteoporosis pancreatic ductal adenocarcinoma ductal breast carcinoma in situ cleidocranial dysplasia osteosarcoma rheumatoid arthritis osteoarthritis psoriatic arthritis osteochondrodysplasia Craniofacial Abnormalities uremia metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome non-small cell lung carcinoma osteoarthritis susceptibility 1 adrenoleukodystrophy osteoporosis pancreatic ductal adenocarcinoma ductal breast carcinoma in situ spondyloarthropathy invasive ductal breast carcinoma malignant glioma medulloblastoma osteoarthritis, hip osteogenesis imperfecta B-cell chronic lymphocytic leukemia pilocytic astrocytoma craniosynostosis sarcoidosis glioblastoma lung adenocarcinoma tuberculosis malignant pancreatic neoplasm mucopolysaccharidosis type 4 osteonecrosis cancer ovarian cancer Crohn disease intellectual disability subependymal giant cell astrocytoma malignant ependymoma ulcerative colitis MALT lymphoma
A	Pharos: P11308	Ewing sarcoma acute myeloid leukemia Neoplastic Processes prostate cancer leukemia lung adenocarcinoma olfactory neuroblastoma ovarian cancer abdominal aortic aneurysm pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer childhood acute lymphoblastic leukemia ductal breast carcinoma in situ gastric carcinoma lung cancer Ewing sarcoma acute myeloid leukemia Neoplastic Processes prostate cancer leukemia lung adenocarcinoma olfactory neuroblastoma ovarian cancer abdominal aortic aneurysm pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer childhood acute lymphoblastic leukemia ductal breast carcinoma in situ gastric carcinoma lung cancer nephrosclerosis osteoarthritis pancreatic intraductal papillary-mucinous carcinoma acute lymphoblastic leukemia breast carcinoma cystic fibrosis interstitial cystitis lung carcinoma non-small cell lung carcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm B-cell acute lymphoblastic leukemia cancer Down syndrome extraskeletal Ewing sarcoma invasive ductal breast 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.