5YUF | pdb_00005yuf

Crystal Structure of PML RING tetramer

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5yufd_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5yufc_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5yufb_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5yufa_	Small proteins	RING/U-box	RING/U-box	RING finger domain, C3HC4	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	RING/U-box like	8039293	3000160	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RING/U-box like	8039293	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RING/U-box like	8039293	3000160	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RING/U-box like	8039293	3000160	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)
D	V-set	e5yufD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
C	V-set	e5yufC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
B	V-set	e5yufB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	Diphthamide_syn	e5yufA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00097	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4)	Zinc finger, C3HC4 type (RING finger)	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many protein ...	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Protein PML	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity transferase activity catalytic activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity transferase activity catalytic activity SUMO transferase activity DNA binding nucleic acid binding SUMO binding protein binding ubiquitin-like protein binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding protein heterodimerization activity protein dimerization activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein homodimerization activity SMAD binding zinc ion binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction signal transduction by p53 class mediator regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling cell adhesion regulation of cell adhesion inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of protein stability regulation of biological quality protein stabilization catabolic process negative regulation of biological process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process modification-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process response to interleukin-4 response to peptide response to chemical response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis cell surface receptor signaling pathway extrinsic apoptotic signaling pathway apoptotic signaling pathway localization macromolecule localization protein-containing complex localization intracellular receptor signaling pathway response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone nuclear receptor-mediated signaling pathway cellular response to hormone stimulus ameboidal-type cell migration cell migration fibroblast migration cell motility establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization intercellular transport import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport cellular response to stress cellular senescence regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process nuclear body organization nucleus organization organelle organization PML body organization response to light stimulus entrainment of circadian clock regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription response to UV protein targeting developmental process cellular developmental process cell differentiation cell fate commitment response to decreased oxygen levels response to hypoxia response to oxygen levels regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus regulation of defense response to virus defense response to virus regulation of response to stress positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus branching involved in mammary gland duct morphogenesis multicellular organismal process mammary gland morphogenesis mammary gland development branching morphogenesis of an epithelial tube gland development multicellular organism development tube morphogenesis gland morphogenesis anatomical structure development animal organ morphogenesis epithelial tube morphogenesis epithelium development tube development animal organ development morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis anatomical structure morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium positive regulation of organelle organization regulation of telomere maintenance positive regulation of cellular component organization telomere organization positive regulation of metabolic process positive regulation of macromolecule metabolic process 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 positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of localization regulation of protein localization positive regulation of protein localization to chromosome, telomeric region protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region protein localization to chromosome positive regulation of protein localization cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway myeloid cell differentiation hemopoiesis cell development negative regulation of translation in response to stress protein biosynthetic process post-transcriptional regulation of gene expression translational initiation regulation of translational initiation negative regulation of gene expression negative regulation of macromolecule biosynthetic process negative regulation of translation in response to oxidative stress cellular response to oxidative stress cellular response to chemical stress negative regulation of translation regulation of translation in response to stress negative regulation of translational initiation in response to stress negative regulation of translational initiation translation regulation of translation in response to oxidative stress response to oxidative stress negative regulation of biosynthetic process regulation of translation regulation of translational initiation in response to stress negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly maintenance of protein location maintenance of protein location in nucleus maintenance of location maintenance of location in cell maintenance of protein location in cell maintenance of protein localization in organelle fibroblast proliferation cell population proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of cytokine production cytokine production regulation of multicellular organismal process regulation of interleukin-1 production negative regulation of cytokine production interleukin-1 beta production negative regulation of multicellular organismal process suppression of viral release by host regulation of programmed cell death positive regulation of apoptotic signaling pathway positive regulation of programmed cell death regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway regulation of double-strand break repair regulation of cellular response to stress DNA repair double-strand break repair regulation of DNA repair DNA damage response proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process negative regulation of telomere maintenance negative regulation of telomere maintenance via telomerase regulation of DNA biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening negative regulation of chromosome organization negative regulation of cellular component organization regulation of telomere maintenance via telomere lengthening DNA biosynthetic process negative regulation of DNA biosynthetic process negative regulation of telomere maintenance via telomere lengthening telomere maintenance via telomerase regulation of telomere maintenance via telomerase negative regulation of organelle organization negative regulation of DNA metabolic process intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway oncogene-induced cell senescence SMAD protein signal transduction intracellular signaling cassette negative regulation of cell population proliferation intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress response to endoplasmic reticulum stress response to ionizing radiation response to gamma radiation regulation of calcium ion transport regulation of calcium ion transport into cytosol monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration transmembrane transport regulation of transmembrane transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport calcium ion transport into cytosol DNA damage response, signal transduction by p53 class mediator signal transduction in response to DNA damage intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway by p53 class mediator regulation of developmental process angiogenesis regulation of vasculature development regulation of anatomical structure morphogenesis system development blood vessel development regulation of multicellular organismal development blood vessel morphogenesis negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis cell cycle regulation of cell cycle intrinsic apoptotic signaling pathway in response to oxidative stress apoptotic process involved in morphogenesis positive regulation of apoptotic process involved in mammary gland involution apoptotic process involved in development positive regulation of developmental process positive regulation of apoptotic process involved in morphogenesis mammary gland involution positive regulation of apoptotic process involved in development apoptotic process involved in mammary gland involution regulation of apoptotic process involved in development tissue remodeling response to leukemia inhibitory factor cellular response to leukemia inhibitory factor negative regulation of cell cycle negative regulation of mitotic cell cycle mitotic cell cycle regulation of mitotic cell cycle chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix nucleolus nucleoplasm organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane endosome membrane early endosome endosome intracellular vesicle early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane vesicle nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR047153	TRIM45/56/19-like	Family
A, B, C, D	IPR057617	PML, C-terminal domain	Domain
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D	IPR021978	PML-like, coiled-coil	Domain
A, B, C, D	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, B, C, D	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B, C, D	IPR000315	B-box-type zinc finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P29590	acute promyelocytic leukemia glioblastoma Stevens-Johnson syndrome bone Paget disease Neoplasms, Second Primary prostate cancer giant cell glioblastoma schizophrenia ovarian cancer acute myeloid leukemia heart disease large cell medulloblastoma medulloblastoma myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm acute promyelocytic leukemia glioblastoma Stevens-Johnson syndrome bone Paget disease Neoplasms, Second Primary prostate cancer giant cell glioblastoma schizophrenia ovarian cancer acute myeloid leukemia heart disease large cell medulloblastoma medulloblastoma myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm cancer ulcerative colitis exfoliation syndrome multiple sclerosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor toxic epidermal necrolysis cutaneous lupus erythematosus head and neck cancer malignant glioma

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.