5J9T | pdb_00005j9t

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)
I	d5j9ti_	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 A]	d5j9ta_	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)
A [auth E]	d5j9te_	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)
L	SCOP2 Family	Yng2-like	8048251	4006027	SCOP2 (2022-06-29)
L	SCOP2 Superfamily	YNG2-like	8055780	3002310	SCOP2 (2022-06-29)
H [auth D]	SCOP2B Superfamily	YNG2-like	8055780	3002310	SCOP2B (2022-06-29)
D [auth H]	SCOP2B Superfamily	YNG2-like	8055780	3002310	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	EPL1 ESA1-binding domain-like	8055777	3002308	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	EPL1 YNG2-binding region-like	8055779	3002309	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)
C [auth G]	SCOP2 Family	EPL1 ESA1-binding domain-like	8045005	4004251	SCOP2 (2022-06-29)
C [auth G]	SCOP2 Family	EPL1 YNG2-binding region-like	8055778	4007655	SCOP2 (2022-06-29)
C [auth G]	SCOP2 Superfamily	EPL1 ESA1-binding domain-like	8055777	3002308	SCOP2 (2022-06-29)
C [auth G]	SCOP2 Superfamily	EPL1 YNG2-binding region-like	8055779	3002309	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036035	3000403	SCOP2B (2022-06-29)
A [auth E]	SCOP2B Superfamily	beta-beta-alpha zinc fingers	8101147	3001077	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)
G [auth C]	Ski2_beta-barrel	e5j9tC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ski2_beta-barrel	ECOD (v294.1)
C [auth G]	Ski2_beta-barrel	e5j9tG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ski2_beta-barrel	ECOD (v294.1)
I	HTH_3	e5j9tI1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: HTH_3	ECOD (v294.1)
E [auth A]	HTH_3	e5j9tA1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: HTH_3	ECOD (v294.1)
A [auth E]	HTH_3	e5j9tE1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: HTH_3	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth H], H [auth D], L	PF12998	Inhibitor of growth proteins N-terminal histone-binding (ING)	Inhibitor of growth proteins N-terminal histone-binding	-	Coiled-coil
B [auth F], F [auth B], J	PF09340	Histone acetyltransferase subunit NuA4 (NuA4)	Histone acetyltransferase subunit NuA4	-	Family
A [auth E], E [auth A], 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], E [auth A], I	PF01853	MOZ/SAS family (MOZ_SAS)	MOZ/SAS family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth H], H [auth D], L	Chromatin modification-related protein YNG2	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	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 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 cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex piccolo histone acetyltransferase complex cytoplasm cytosol protein-DNA complex nucleosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth G], G [auth C], K	Enhancer of polycomb-like protein 1	-	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 transcription by RNA polymerase II 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 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 transcription by RNA polymerase II 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 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 positive regulation of autophagy catabolic process macroautophagy autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of macroautophagy positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of cellular process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex protein-DNA complex nucleosome piccolo histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth F], F [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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair RNA metabolic process cellular response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair 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 cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex H3 histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex H3 histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex NuA3 histone acetyltransferase complex intracellular protein-containing complex 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
A [auth E], E [auth A], I	Histone acetyltransferase ESA1	transcription regulator activity transcription coregulator activity 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 transcription regulator activity transcription coregulator activity 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 binding peptide 2-hydroxyisobutyryltransferase activity peptide crotonyltransferase activity histone crotonyltransferase activity histone H4 acetyltransferase activity	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 metabolic process cellular process macromolecule metabolic process 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 metabolic process cellular process macromolecule metabolic process neutral lipid metabolic process neutral lipid biosynthetic process regulation of cellular 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 acylglycerol biosynthetic process regulation of primary metabolic 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 biosynthetic process regulation of biological process biological regulation regulation of triglyceride biosynthetic process positive regulation of triglyceride biosynthetic process glycerolipid biosynthetic process positive regulation of lipid biosynthetic process glycerolipid metabolic process regulation of lipid biosynthetic process acylglycerol metabolic process regulation of metabolic process lipid metabolic process DNA-templated transcription elongation positive regulation of autophagy catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process regulation of macroautophagy positive regulation of macroautophagy process utilizing autophagic mechanism cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell cycle regulation of cell cycle negative regulation of biological process nucleolar chromatin organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis rDNA heterochromatin formation 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 nucleus organization organelle organization negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleolus organization facultative heterochromatin formation negative regulation of gene expression, epigenetic	protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex protein-DNA complex nucleosome piccolo histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth H], H [auth D], L	IPR001965	Zinc finger, PHD-type	Domain
D [auth H], H [auth D], L	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
D [auth H], H [auth D], L	IPR028651	ING family	Family
D [auth H], H [auth D], L	IPR019787	Zinc finger, PHD-finger	Domain
D [auth H], H [auth D], L	IPR024610	Inhibitor of growth protein, N-terminal histone-binding	Domain
D [auth H], H [auth D], L	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
D [auth H], H [auth D], L	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
C [auth G], G [auth C], K	IPR024943	Enhancer of polycomb protein	Family
C [auth G], G [auth C], K	IPR019542	Enhancer of polycomb-like, N-terminal	Domain
B [auth F], F [auth B], J	IPR015418	Chromatin modification-related protein Eaf6	Family
A [auth E], E [auth A], I	IPR002717	Histone acetyltransferase domain, MYST-type	Domain
A [auth E], E [auth A], I	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth E], E [auth A], I	IPR050603	MYST family histone acetyltransferases	Family
A [auth E], E [auth A], I	IPR000953	Chromo/chromo shadow domain	Domain
A [auth E], E [auth A], I	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth E], E [auth A], I	IPR025995	RNA binding activity-knot of a chromodomain	Domain
A [auth E], E [auth A], I	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A [auth E], E [auth A], I	IPR040706	MYST, zinc finger domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth E], E [auth A], 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.