4M6B | pdb_00004m6b

Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer

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)
C [auth D]	d4m6bd1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4m6ba1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ], 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)
C [auth D]	SCOP2B Superfamily	Core histone-like	8103853	3001387	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Core histone-like	8067142	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8067142	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8103853	3001387	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 [auth D]		e4m6bD3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: CoV_NSP4_C	F:	ECOD (20:10:01)
A		e4m6bA1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Rep-A_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, C [auth D]	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D [auth F]	Helicase SWR1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding histone binding DNA binding protein-containing complex binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity catalytic activity, acting on a protein catalytic activity, acting on a nucleic acid histone chaperone activity ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA protein carrier chaperone ATP-dependent histone chaperone activity ATP-dependent H2AZ histone chaperone activity molecular carrier activity molecular adaptor activity structural molecule activity nucleic acid conformation isomerase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to stimulus response to stimulus DNA recombination DNA metabolic process cellular response to stress DNA damage response response to stress recombinational repair DNA repair	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm membraneless organelle SWI/SNF superfamily-type complex INO80-type complex catalytic complex intracellular membraneless organelle chromatin intracellular membrane-bounded organelle Swr1 complex organelle lumen organelle nuclear lumen cytoplasm cytosol
A, C [auth D]	Chimera protein of Histone H2B.1 and Histone H2A.Z	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin chromatin binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin chromatin binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding identical protein 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 DNA damage tolerance DNA replication cellular response to stress DNA damage response response to stress negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular component organization chromatin organization cellular component organization or biogenesis catabolic process macromolecule catabolic process RNA catabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process nuclear-transcribed mRNA catabolic process, non-stop decay mRNA metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression nucleic acid catabolic process cellular component biogenesis cellular component assembly chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression, epigenetic transcription elongation by RNA polymerase II DNA-templated transcription elongation constitutive heterochromatin formation silent mating-type cassette heterochromatin formation	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 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 euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D [auth F]	IPR001650	Helicase, C-terminal domain-like	Domain
B [auth C], D [auth F]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B [auth C], D [auth F]	IPR050520	INO80/SWR1 chromatin remodeling helicase	Family
B [auth C], D [auth F]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
B [auth C], D [auth F]	IPR014012	Helicase/SANT-associated domain	Domain
B [auth C], D [auth F]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
B [auth C], D [auth F]	IPR000330	SNF2, N-terminal domain	Domain
B [auth C], D [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth D]	IPR009072	Histone-fold	Homologous Superfamily
A, C [auth D]	IPR000558	Histone H2B	Family
A, C [auth D]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, C [auth D]	IPR055333	Histone H2B, conserved site	Conserved Site
A, C [auth D]	IPR009072	Histone-fold	Homologous Superfamily
A, C [auth D]	IPR002119	Histone H2A	Family
A, C [auth D]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, C [auth D]	IPR032454	Histone H2A, C-terminal domain	Domain
A, C [auth D]	IPR032458	Histone H2A conserved site	Conserved Site

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.