5J9U

Crystal structure of the NuA4 core complex

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
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 [auth E]	d5j9ue_	Alpha and beta proteins (a+b)	Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	N-acetyl transferase, NAT	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D [auth A]	d5j9ua_	Alpha and beta proteins (a+b)	Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	N-acetyl transferase, NAT	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E [auth I]	d5j9ui_	Alpha and beta proteins (a+b)	Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	N-acetyl transferase, NAT	automated matches	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)
A [auth E]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
B [auth F]	SCOP2 Family	NuA4-like	8044704	4004090	SCOP2 (2022-06-29)
B [auth F]	SCOP2 Superfamily	NuA4-like	8052030	3002083	SCOP2 (2022-06-29)
C [auth G]	SCOP2B Superfamily	EPL1 YNG2-binding region-like	8055779	3002309	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	EPL1 ESA1-binding domain-like	8055777	3002308	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	EPL1 YNG2-binding region-like	8055779	3002309	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	EPL1 ESA1-binding domain-like	8055777	3002308	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	EPL1 ESA1-binding domain-like	8055777	3002308	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	EPL1 YNG2-binding region-like	8055779	3002309	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	YNG2-like	8055780	3002310	SCOP2B (2022-06-29)
K [auth H]	SCOP2B Superfamily	YNG2-like	8055780	3002310	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	YNG2-like	8055780	3002310	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 [auth E]	PF01853	e5j9uE2	A: alpha arrays	X: HTH	H: HTH	T: HAT1, C-terminal domain	F: PF01853	ECOD (1.6)
A [auth E]	PF01853	e5j9uE1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: PF01853	ECOD (1.6)
A [auth E]	PF17772	e5j9uE3	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: PF17772	ECOD (1.6)
D [auth A]	PF01853	e5j9uA2	A: alpha arrays	X: HTH	H: HTH	T: HAT1, C-terminal domain	F: PF01853	ECOD (1.6)
D [auth A]	PF01853	e5j9uA3	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: PF01853	ECOD (1.6)
D [auth A]	PF17772	e5j9uA1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: PF17772	ECOD (1.6)
E [auth I]	PF01853	e5j9uI1	A: alpha arrays	X: HTH	H: HTH	T: HAT1, C-terminal domain	F: PF01853	ECOD (1.6)
E [auth I]	PF01853	e5j9uI3	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: PF01853	ECOD (1.6)
E [auth I]	PF17772	e5j9uI2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: PF17772	ECOD (1.6)
C [auth G]	PF10513	e5j9uG1	A: alpha arrays	X: Enhancer of polycomb-like protein 1 (Epl1) N-terminal domain (From Topology)	H: Enhancer of polycomb-like protein 1 (Epl1) N-terminal domain (From Topology)	T: Enhancer of polycomb-like protein 1 (Epl1) N-terminal domain	F: PF10513	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], D [auth A], E [auth I]	PF17772	MYST family zinc finger domain (zf-MYST)	MYST family zinc finger domain	This zinc finger domain is found in the MYST family of histone acetyltransferases [1].	Domain
A [auth E], D [auth A], E [auth I]	PF01853	MOZ/SAS family (MOZ_SAS)	MOZ/SAS family	-	Family
B [auth F], I [auth B], J	PF09340	Histone acetyltransferase subunit NuA4 (NuA4)	Histone acetyltransferase subunit NuA4	-	Family
C [auth G], F [auth N], G [auth C]	PF10513	Enhancer of polycomb-like (EPL1)	Enhancer of polycomb-like	-	Family
H [auth D], K [auth H], L [auth K]	PF12998	Inhibitor of growth proteins N-terminal histone-binding (ING)	Inhibitor of growth proteins N-terminal histone-binding	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], D [auth A], E [auth I]	Histone acetyltransferase ESA1	transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity catalytic activity, acting on a protein N-acetyltransferase activity acyltransferase activity transferase activity peptide N-acetyltransferase activity histone acetyltransferase activity acetyltransferase activity peptide-lysine-N-acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity catalytic activity, acting on a protein N-acetyltransferase activity acyltransferase activity transferase activity peptide N-acetyltransferase activity histone acetyltransferase activity acetyltransferase activity peptide-lysine-N-acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity peptide 2-hydroxyisobutyryltransferase activity peptide crotonyltransferase activity histone crotonyltransferase activity histone H4 acetyltransferase activity histone H4K16 acetyltransferase activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process neutral lipid metabolic process neutral lipid biosynthetic process regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process positive regulation of cellular metabolic process acylglycerol biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process triglyceride metabolic process triglyceride biosynthetic process positive regulation of lipid metabolic process positive regulation of cellular process regulation of triglyceride biosynthetic process positive regulation of triglyceride biosynthetic process glycerolipid biosynthetic process positive regulation of lipid biosynthetic process cellular lipid metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process acylglycerol metabolic process positive regulation of cellular biosynthetic process lipid metabolic process DNA-templated transcription elongation catabolic process macroautophagy autophagy regulation of autophagy cellular catabolic process positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation positive regulation of RNA biosynthetic process cell cycle regulation of cell cycle nucleolar chromatin organization protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis rDNA heterochromatin formation heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of gene expression nucleus organization organelle organization nucleolus organization facultative heterochromatin formation negative regulation of gene expression, epigenetic	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle nucleosome piccolo histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth F], I [auth B], J	Chromatin modification-related protein EAF6	-	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cellular biosynthetic process cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity H3 histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity H3 histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex NuA3 histone acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle NuA3a histone acetyltransferase complex NuA3b histone acetyltransferase complex NuA4 histone acetyltransferase complex H4/H2A histone acetyltransferase complex H4 histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth G], F [auth N], G [auth C]	Enhancer of polycomb-like protein 1	-	cellular process cell cycle regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process cellular process cell cycle regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic 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 cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process catabolic process macroautophagy autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle nucleosome piccolo histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
H [auth D], K [auth H], L [auth K]	Chromatin modification-related protein YNG2	methylated histone binding protein binding binding modification-dependent protein binding histone binding methylation-dependent protein binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair sexual reproduction reproductive process meiotic cell cycle cell cycle protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex NuA4 histone acetyltransferase complex chromatin chromosome transferase complex cellular anatomical entity H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle piccolo histone acetyltransferase complex cytoplasm cytosol nucleosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], D [auth A], E [auth I]	IPR002717	Histone acetyltransferase domain, MYST-type	Domain
A [auth E], D [auth A], E [auth I]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth E], D [auth A], E [auth I]	IPR000953	Chromo/chromo shadow domain	Domain
A [auth E], D [auth A], E [auth I]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth E], D [auth A], E [auth I]	IPR025995	RNA binding activity-knot of a chromodomain	Domain
A [auth E], D [auth A], E [auth I]	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A [auth E], D [auth A], E [auth I]	IPR040706	MYST, zinc finger domain	Domain
B [auth F], I [auth B], J	IPR015418	Chromatin modification-related protein Eaf6	Family
C [auth G], F [auth N], G [auth C]	IPR024943	Enhancer of polycomb protein	Family
C [auth G], F [auth N], G [auth C]	IPR019542	Enhancer of polycomb-like, N-terminal	Domain
H [auth D], K [auth H], L [auth K]	IPR001965	Zinc finger, PHD-type	Domain
H [auth D], K [auth H], L [auth K]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
H [auth D], K [auth H], L [auth K]	IPR028651	ING family	Family
H [auth D], K [auth H], L [auth K]	IPR019787	Zinc finger, PHD-finger	Domain
H [auth D], K [auth H], L [auth K]	IPR024610	Inhibitor of growth protein, N-terminal histone-binding	Domain
H [auth D], K [auth H], L [auth K]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
H [auth D], K [auth H], L [auth K]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth E], D [auth A], E [auth I]	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 R01GM133198.