2RNW

The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the Human Transcriptional Co-Activators PCAf and CBP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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	d2rnwa2	All alpha proteins	Bromodomain-like	Bromodomain	Bromodomain	P300/CAF histone acetyltransferase bromodomain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2rnwa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	SCOP2B Superfamily	Bromodomain	8033300	3001843	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)
A	Bromodomain	e2rnwA1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00439	Bromodomain (Bromodomain)	Bromodomain	Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone acetyltransferase PCAF	acetyltransferase activity N-acetyltransferase activity acyltransferase activity diamine N-acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity N-acyltransferase activity enzyme regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity acetyltransferase activity N-acetyltransferase activity acyltransferase activity diamine N-acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity N-acyltransferase activity enzyme regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity molecular function regulator activity cyclin-dependent protein serine/threonine kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity histone deacetylase binding protein binding binding enzyme binding catalytic activity, acting on a protein histone H3 acetyltransferase activity peptide N-acetyltransferase activity histone acetyltransferase activity histone H3K9 acetyltransferase activity peptide-lysine-N-acetyltransferase activity histone modifying activity lysine N-acetyltransferase activity, acting on acetyl phosphate as donor transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding transcription coactivator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding kinase binding protein kinase binding histone acetyltransferase binding transcription factor binding DNA-binding transcription factor binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of cellular process positive regulation of biological 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 positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process 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 biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process peptidyl-lysine acetylation peptidyl-lysine modification protein acylation protein acetylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process positive regulation of fatty acid biosynthetic process regulation of small molecule metabolic process positive regulation of lipid metabolic process small molecule metabolic process positive regulation of fatty acid metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process positive regulation of lipid biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process lipid metabolic process behavior system process learning or memory nervous system process cognition memory regulation of cytoskeleton organization negative regulation of centriole replication regulation of cellular component organization microtubule cytoskeleton organization negative regulation of biological process membraneless organelle assembly negative regulation of cell cycle negative regulation of organelle assembly cellular component biogenesis centrosome duplication negative regulation of centrosome cycle cellular component assembly centrosome cycle negative regulation of cellular process cell cycle negative regulation of centrosome duplication regulation of cell cycle regulation of centriole replication centriole replication cell cycle process centriole assembly microtubule organizing center organization organelle assembly negative regulation of cellular component organization regulation of cell cycle process negative regulation of cytoskeleton organization regulation of centrosome cycle regulation of microtubule-based process negative regulation of cell cycle process regulation of cellular component biogenesis regulation of organelle organization organelle organization negative regulation of organelle organization regulation of centrosome duplication regulation of organelle assembly microtubule-based process cytoskeleton organization cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress regulation of neuron projection development positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of molecular function regulation of catalytic activity regulation of transferase activity regulation of protein ADP-ribosylation limb development appendage development regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription monosaccharide metabolic process carbohydrate metabolic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process glucose metabolic process cell division regulation of cell division regulation of transcription from RNA polymerase II promoter by glucose carbon catabolite regulation of transcription positive regulation of transcription by glucose regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription response to nutrient levels positive regulation of DNA-templated transcription positive regulation of transcription from RNA polymerase II promoter by glucose response to nutrient positive regulation of RNA biosynthetic process cellular response to nutrient regulation of transcription by glucose negative regulation of RNA biosynthetic 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 cellular response to stress regulation of response to stress DNA repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of DNA metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of gluconeogenesis positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process ribonucleotide catabolic process pyridine nucleotide catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process regulation of generation of precursor metabolites and energy positive regulation of phosphate metabolic process nucleoside phosphate catabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process positive regulation of nucleotide catabolic process glycolytic process regulation of phosphate metabolic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process positive regulation of phosphorus metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process positive regulation of ATP metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of phosphorus metabolic process regulation of nucleotide catabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process ATP metabolic process catabolic process positive regulation of nucleotide metabolic process positive regulation of purine nucleotide catabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process ribonucleoside triphosphate metabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process positive regulation of glycolytic process ADP catabolic process generation of precursor metabolites and energy regulation of catabolic process regulation of glycolytic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of catabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process ribonucleoprotein complex biogenesis regulation of ribosome biogenesis rRNA processing ribosome biogenesis RNA processing rRNA metabolic process regulation of rRNA processing negative regulation of gene expression negative regulation of ribosome biogenesis negative regulation of rRNA processing N-terminal peptidyl-lysine acetylation protein maturation N-terminal protein amino acid modification N-terminal protein amino acid acetylation negative regulation of catalytic activity regulation of cyclin-dependent protein kinase activity negative regulation of kinase activity negative regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity negative regulation of protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of kinase activity negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cyclin-dependent protein serine/threonine kinase activity negative regulation of protein serine/threonine kinase activity negative regulation of cyclin-dependent protein kinase activity negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation regulation of tube diameter regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasodilation blood circulation regulation of anatomical structure size macromolecule deacylation protein deacetylation regulation of tubulin deacetylation protein deacylation regulation of protein deacetylation tubulin deacetylation rhythmic process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation cellular response to parathyroid hormone stimulus response to endogenous stimulus cellular response to endogenous stimulus response to parathyroid hormone response to hormone cellular response to hormone stimulus regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process cellular response to nitrogen compound response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus internal peptidyl-lysine acetylation internal protein amino acid acetylation RNA splicing regulation of RNA splicing establishment of organelle localization regulation of localization mitotic metaphase chromosome alignment localization regulation of attachment of mitotic spindle microtubules to kinetochore establishment of localization in cell chromosome segregation attachment of mitotic spindle microtubules to kinetochore sister chromatid segregation regulation of chromosome organization establishment of localization regulation of mitotic sister chromatid segregation mitotic cell cycle process establishment of chromosome localization regulation of chromosome segregation cellular localization mitotic cell cycle metaphase chromosome alignment chromosome localization organelle localization mitotic sister chromatid segregation regulation of attachment of spindle microtubules to kinetochore positive regulation of cell cycle process positive regulation of chromosome segregation mitotic nuclear division attachment of spindle microtubules to kinetochore organelle fission positive regulation of attachment of spindle microtubules to kinetochore chromosome organization positive regulation of cell cycle nuclear division regulation of sister chromatid segregation positive regulation of attachment of mitotic spindle microtubules to kinetochore nuclear chromosome segregation regulation of metaphase plate congression	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton actomyosin cytoplasm cytosol protein-containing complex catalytic complex peptidase complex intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton actomyosin cytoplasm cytosol protein-containing complex catalytic complex peptidase complex chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex ATAC complex sarcomere contractile muscle fiber A band supramolecular fiber myofibril supramolecular polymer supramolecular complex I band centrosome microtubule organizing center microtubule cytoskeleton mitotic spindle spindle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome
B	Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin oxidoreductase activity, acting on metal ions oxidoreductase activity oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor cupric reductase (NADH) activity catalytic activity	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary 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 biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary 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 biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process 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 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 inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy 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 transcription by RNA polymerase I positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process sexual sporulation resulting in formation of a cellular spore sexual reproduction reproductive process meiotic cell cycle developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis sexual sporulation anatomical structure formation involved in morphogenesis anatomical structure development sporulation cell cycle cellular response to stimulus global genome nucleotide-excision repair response to stimulus DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle membraneless organelle nuclear lumen replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork CENP-A containing chromatin protein-DNA complex nucleosome chromatin chromosomal region chromosome, centromeric core domain CENP-A containing nucleosome chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018359	Bromodomain, conserved site	Conserved Site
A	IPR000182	GNAT domain	Domain
A	IPR009464	PCAF, N-terminal	Domain
A	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A	IPR016376	Histone acetyltransferase GCN5/PCAF	Family
A	IPR001487	Bromodomain	Domain
A	IPR037800	Histone acetyltransferase GCN5	Family
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Histone H2A/H2B/H3	Domain
B	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92831	pilocytic astrocytoma astrocytic tumor drug dependence invasive ductal breast carcinoma lung cancer MALT lymphoma non-small cell lung carcinoma ovarian cancer rheumatoid arthritis breast cancer ductal breast carcinoma in situ large cell medulloblastoma malignant colon neoplasm medulloblastoma oligodendroglioma pilocytic astrocytoma astrocytic tumor drug dependence invasive ductal breast carcinoma lung cancer MALT lymphoma non-small cell lung carcinoma ovarian cancer rheumatoid arthritis breast cancer ductal breast carcinoma in situ large cell medulloblastoma malignant colon neoplasm medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma spina bifida Down syndrome glioblastoma lung adenocarcinoma malignant ependymoma Mood Disorders osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.