9R5S | pdb_00009r5s

Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth D], J [auth H]	Histone H2B 1.1	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	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
K [auth W]	Chromo domain-containing protein 1	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA ATP-dependent chromatin remodeler activity 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 rDNA 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	cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing 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 cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing 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 regulation of cellular process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process DNA-templated transcriptional start site selection transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription, start site selection transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation regulation of gene expression biosynthetic process regulation of transcription initiation by RNA polymerase II regulation of macromolecule biosynthetic process transcriptional start site selection at RNA polymerase II promoter regulation of DNA-templated transcription regulation of metabolic process DNA-templated transcription termination termination of RNA polymerase II transcription cellular component organization organelle organization chromosome organization sister chromatid cohesion cellular component organization or biogenesis cell cycle cell cycle process regulation of chromatin organization regulation of cellular component organization chromatin organization transcription by RNA polymerase I termination of RNA polymerase I transcription DNA recombination recombinational repair double-strand break repair via homologous recombination transcription elongation by RNA polymerase II DNA-templated transcription elongation negative regulation of biological process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication negative regulation of DNA replication negative regulation of metabolic process DNA replication regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication protein-DNA complex organization protein-containing complex organization chromatin remodeling nucleosome organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SLIK (SAGA-like) complex intracellular protein-containing complex nucleolar chromatin nucleus membrane-enclosed lumen nuclear chromosome nucleolus intracellular organelle lumen organelle lumen nuclear lumen peptidase complex SAGA complex site of double-strand break site of DNA damage
E [auth C], I [auth G]	Histone H2A type 1	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	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 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 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	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
D [auth B], H [auth F]	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	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 process cellular component organization or biogenesis nucleosome assembly nucleosome organization	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 [auth A], G [auth E]	Histone H3.2	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	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 membrane-enclosed lumen 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 membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth J]	DNA (160-MER)	-	-	-
A [auth I]	DNA (160-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth D], J [auth H]	IPR009072	Histone-fold	Homologous Superfamily
F [auth D], J [auth H]	IPR055333	Histone H2B, conserved site	Conserved Site
F [auth D], J [auth H]	IPR000558	Histone H2B	Family
F [auth D], J [auth H]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
K [auth W]	IPR000330	SNF2, N-terminal	Domain
K [auth W]	IPR023780	Chromo domain	Domain
K [auth W]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
K [auth W]	IPR023779	Chromo domain, conserved site	Conserved Site
K [auth W]	IPR041150	Chromodomain helicase DNA-binding domain	Domain
K [auth W]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
K [auth W]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
K [auth W]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
K [auth W]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
K [auth W]	IPR000953	Chromo/chromo shadow domain	Domain
K [auth W]	IPR001650	Helicase, C-terminal domain-like	Domain
K [auth W]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
K [auth W]	IPR056302	ATP-dependent helicase CHD1-2/hrp3, HTH domain	Domain
K [auth W]	IPR025260	Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain	Domain
E [auth C], I [auth G]	IPR009072	Histone-fold	Homologous Superfamily
E [auth C], I [auth G]	IPR002119	Histone H2A	Family
E [auth C], I [auth G]	IPR032454	Histone H2A, C-terminal domain	Domain
E [auth C], I [auth G]	IPR032458	Histone H2A conserved site	Conserved Site
E [auth C], I [auth G]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D [auth B], H [auth F]	IPR009072	Histone-fold	Homologous Superfamily
D [auth B], H [auth F]	IPR001951	Histone H4	Family
D [auth B], H [auth F]	IPR035425	CENP-T/Histone H4, histone fold	Domain
D [auth B], H [auth F]	IPR019809	Histone H4, conserved site	Conserved Site
D [auth B], H [auth F]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C [auth A], G [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth A], G [auth E]	IPR000164	Histone H3/CENP-A	Family
C [auth A], G [auth E]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9R5S | pdb_00009r5s

Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

9R5S | pdb_00009r5s