2QIC | pdb_00002qic

Crystal Structure of the ING1 PHD Finger in complex with a Histone H3K4ME3 peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2qica_	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	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)
A	SCOP2 Family	PHD domain	8087158	4003778	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FYVE/PHD zinc finger	8087159	3001459	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Gal-bind_lectin	e2qicA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: Gal-bind_lectin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	H3K4ME3 PEPTIDE	-	-	-
A	Inhibitor of growth protein 1	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication cellular process response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of programmed cell death cell death programmed cell death negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process developmental process multicellular organismal process regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number negative regulation of developmental process negative regulation of stem cell population maintenance negative regulation of multicellular organismal process 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 negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II 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 establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR028651	ING family	Family
A	IPR028643	Inhibitor of growth protein 1, PHD-type zinc finger	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR024610	Inhibitor of growth protein, N-terminal histone-binding	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UK53	head and neck squamous cell carcinoma contact dermatitis Squamous cell carcinoma of the hypopharynx astrocytic tumor gastric cancer malignant mesothelioma oral cavity squamous cell carcinoma squamous cell carcinoma of lip cancer gastric neoplasm hereditary diffuse gastric adenocarcinoma osteosarcoma glioblastoma laryngeal squamous cell carcinoma medulloblastoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.