4PSX | pdb_00004psx

Crystal structure of histone acetyltransferase complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d4psxe_	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4psxb_	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d4psxd_	Alpha and beta proteins (a+b)	Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	N-acetyl transferase, NAT	Histone acetyltransferase HAT1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4psxa_	Alpha and beta proteins (a+b)	Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	N-acetyl transferase, NAT	Histone acetyltransferase HAT1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	WD40 repeat-like	8053351	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8053351	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036033	3000403	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036033	3000403	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)
C	Serpin	e4psxC01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Serpin	ECOD (v294.1)
E	YajR_YAM	e4psxE1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: YajR_YAM	ECOD (v294.1)
B	YajR_YAM	e4psxB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: YajR_YAM	ECOD (v294.1)
D	YajR_YAM	e4psxD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: YajR_YAM	ECOD (v294.1)
A	YajR_YAM	e4psxA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: YajR_YAM	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	3.90.360.10	Alpha Beta	Alpha-Beta Complex	Histone Acetyltransferase	domain 1	CATH (4.3.0)
D	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)
D	1.10.10.390	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A	3.90.360.10	Alpha Beta	Alpha-Beta Complex	Histone Acetyltransferase	domain 1	CATH (4.3.0)
A	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)
A	1.10.10.390	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
B, E	PF12265	Histone-binding protein RBBP4 or subunit C of CAF1 complex (CAF1C_H4-bd)	Histone-binding protein RBBP4 or subunit C of CAF1 complex	-	Repeat
B, E	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
A, D	PF21184	Fungal HAT1, C-terminal (HAT1_C_fung)	Fungal HAT1, C-terminal	Histone acetyltransferase type B catalytic subunit (HAT1) is the catalytic subunit of the histone acetylase B (HAT-B) complex (composed on HAT1 and HAT2 at least) [1,2]. It DNA double-strand break repair. Yeast HAT1 specifically acetylates H4 at Lys5 ...	Histone acetyltransferase type B catalytic subunit (HAT1) is the catalytic subunit of the histone acetylase B (HAT-B) complex (composed on HAT1 and HAT2 at least) [1,2]. It DNA double-strand break repair. Yeast HAT1 specifically acetylates H4 at Lys5 and Lys12 residues. The C-terminal domain of HAT1 (this entry) is highly variable and not required for HAT activity [1]. It consists of a bundle of helices and a short beta-strand. This entry includes HAT1 from Fungi.	Domain
A, D	PF10394	Histone acetyl transferase HAT1 N-terminus (Hat1_N)	Histone acetyl transferase HAT1 N-terminus	This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (Pfam:PF00583) domain. It seems to be motifs C and D of the structure. Histon ...	This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (Pfam:PF00583) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated [1].	Domain
A, D	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth Y], H [auth P]	Histone H3	DNA binding 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 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 CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region chromosome, centromeric core domain CENP-A containing nucleosome chromosome, centromeric region
C, F	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	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 protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization 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 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 regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	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 protein-DNA complex nucleosome chromatin chromosome
B, E	Histone acetyltransferase type B subunit 2	protein binding binding histone binding	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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process subtelomeric heterochromatin formation negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	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 Rpd3L-Expanded complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex nucleoplasm organelle lumen nuclear lumen cytoplasm Sin3-type complex Rpd3L complex chromosome, telomeric region chromosomal region
A, D	Histone acetyltransferase type B catalytic subunit	protein binding binding histone binding protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups protein binding binding histone binding protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity chromatin binding histone H4 acetyltransferase activity	subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus double-strand break repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair	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 cytoplasm chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth Y], H [auth P]	IPR009072	Histone-fold	Homologous Superfamily
G [auth Y], H [auth P]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
G [auth Y], H [auth P]	IPR000164	Histone H3/CENP-A	Family
C, F	IPR009072	Histone-fold	Homologous Superfamily
C, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
C, F	IPR001951	Histone H4	Family
C, F	IPR019809	Histone H4, conserved site	Conserved Site
B, E	IPR050459	WD repeat RBAP46/RBAP48/MSI1	Family
B, E	IPR019775	WD40 repeat, conserved site	Conserved Site
B, E	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, E	IPR022052	Histone-binding protein RBBP4-like, N-terminal	Domain
B, E	IPR001680	WD40 repeat	Repeat
B, E	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D	IPR019467	Histone acetyl transferase HAT1 N-terminal	Domain
A, D	IPR037113	Histone acetyl transferase 1, N-terminal domain superfamily	Homologous Superfamily
A, D	IPR017380	Histone acetyltransferase type B, catalytic subunit	Family
A, D	IPR000182	GNAT domain	Domain
A, D	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A, D	IPR013523	Histone acetyltransferase HAT1, C-terminal	Homologous Superfamily

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.