Annotations: 5ZBA

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Core histone-like	8036586	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8036585	3001387	SCOP2B (2022-06-29)
B	SCOP2 Family	ASF1-like	8067064	4007545	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ASF1-like	8067065	3002057	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e5zbaD1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F:	ECOD (v294.2)
C		e5zbaC1	A: beta barrels	X: Surp module (SWAP domain)	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (v294.2)
B		e5zbaB1	A: beta barrels	X: Surp module (SWAP domain)	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (v294.2)
A		e5zbaA1	A: beta barrels	X: Surp module (SWAP domain)	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F:	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
C	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
B	2.60.40.1490	Mainly Beta	Sandwich	Immunoglobulin-like	Histone chaperone ASF1-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
B	PF04729	ASF1 like histone chaperone (ASF1_hist_chap)	ASF1 like histone chaperone	-	Family
A	PF08214	Histone acetyltransferase KAT11-type domain (HAT_KAT11)	Histone acetyltransferase KAT11-type domain	This entry represents a histone acetyltransferase catalytic domain found in fungal proteins, including RTT109 (also known as KAT11) from budding and fission yeasts and Candida species. This domain catalyses the acetylation of lysine residues on histo ...	This entry represents a histone acetyltransferase catalytic domain found in fungal proteins, including RTT109 (also known as KAT11) from budding and fission yeasts and Candida species. This domain catalyses the acetylation of lysine residues on histone H3, including H3K56, H3K9, H3K14, H3K23 and H3K27 [1,2]. The domain functions within a complex with histone chaperones such as VPS75 that regulate substrate specificity [3]. Acetylation of H3K56 by this domain promotes nucleosome assembly, DNA repair and transcriptional regulation during S-phase [1,2]. The domain is also found in other histone acetyltransferases including p300/CBP which share a similar fold but differ in catalytic properties and cofactor requirements [3]. Members of this family show conservation across most eukaryotic fungi.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	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	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	Histone H3	protein heterodimerization activity protein binding binding protein dimerization activity structural molecule activity structural constituent of chromatin DNA binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding identical protein binding protein heterodimerization activity protein binding binding protein dimerization activity structural molecule activity structural constituent of chromatin DNA binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding identical protein binding 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	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 organelle assembly protein-containing complex organization chromosome organization 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 organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy mitotic nuclear division mitotic metaphase chromosome alignment organelle fission sister chromatid segregation mitotic cell cycle metaphase chromosome alignment localization nuclear division mitotic cell cycle process chromosome localization organelle localization nuclear chromosome segregation mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process cellular response to stimulus global genome nucleotide-excision repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress macromolecule metabolic process DNA repair nucleolar large rRNA transcription by RNA polymerase I 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 transcription by RNA polymerase I rRNA transcription 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 negative regulation of biological process chromatin organization negative regulation of cellular process chromatin remodeling 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic 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	protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain cellular anatomical structure CENP-A containing nucleosome organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain cellular anatomical structure CENP-A containing nucleosome organelle membraneless organelle chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	Histone chaperone asf1	protein binding binding histone binding enzyme regulator activity enzyme activator activity molecular function activator activity acetyltransferase activator activity molecular function regulator activity	cellular response to stimulus cellular response to stress response to stimulus response to stress cellular 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 response to stimulus cellular response to stress response to stimulus response to stress cellular 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 subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process negative regulation of cellular process 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process DNA replication-dependent chromatin assembly silent mating-type cassette heterochromatin formation transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process positive regulation of transcription by RNA polymerase II nucleic acid metabolic process positive regulation of RNA metabolic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component disassembly protein-DNA complex disassembly protein-containing complex disassembly nucleosome disassembly	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 intracellular protein-containing complex cytoplasm cytosol chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	DNA damage response protein Rtt109, putative	protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity histone H3 acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone H3K56 acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR009072	Histone-fold	Homologous Superfamily
D	IPR035425	CENP-T/Histone H4, histone fold	Domain
D	IPR001951	Histone H4	Family
D	IPR019809	Histone H4, conserved site	Conserved Site
C	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C	IPR000164	Histone H3/CENP-A	Family
C	IPR009072	Histone-fold	Homologous Superfamily
B	IPR017282	Histone deposition protein Asf1	Family
B	IPR036747	Histone chaperone ASF1-like superfamily	Homologous Superfamily
B	IPR006818	Histone chaperone ASF1-like	Family
A	IPR013178	Histone acetyltransferase CBP/p300	Family
A	IPR051236	Histone acetyltransferase RTT109-like	Family
A	IPR016849	Histone acetyltransferase Rtt109	Family

Protein Modification Annotation

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

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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.