6G0L

Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nucleosome core histones	8070520	4000793	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Core histone-like	8070521	3001387	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8070521	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
D	SCOP2 Family	Nucleosome core histones	8066272	4000793	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Core histone-like	8066273	3001387	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	Chromo domain-like	8039987	3000161	SCOP2B (2022-06-29)
L [auth W]	SCOP2B Superfamily	Chromo domain-like	8039987	3000161	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	Histone	e6g0lA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e6g0lE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B	Histone_1	e6g0lB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
F	Histone_1	e6g0lF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C	Histone_1	e6g0lC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
D	Histone	e6g0lD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e6g0lH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
G	Histone_1	e6g0lG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
K [auth M]	Chromo	e6g0lM1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
K [auth M]	SLIDE_1	e6g0lM2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: SLIDE_1	ECOD (1.6)
K [auth M]	SNF2_N	e6g0lM5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SNF2_N	ECOD (1.6)
K [auth M]	KOG0384_1,Helicase_C	e6g0lM4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOG0384_1,Helicase_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
B, F	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
C	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
G	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
K [auth M], L [auth W]	PF18196	Chromodomain helicase DNA-binding domain 1 (Cdh1_DBD_1)	Chromodomain helicase DNA-binding domain 1	This domain can be found in chromodomain helicase DNA-binding protein 1 (Chd1) present in Saccharomyces cerevisiae. Cdh1 proteins have been associated with the efficient assembly and spacing of nucleosomes. The domain consists of four helices, alpha ...	This domain can be found in chromodomain helicase DNA-binding protein 1 (Chd1) present in Saccharomyces cerevisiae. Cdh1 proteins have been associated with the efficient assembly and spacing of nucleosomes. The domain consists of four helices, alpha helix 1-4, and can be divided into regions SANT, HL1 and the beta-linker. The HL1 region comprises of some 40 residues specific to budding yeast that are unlikely to form such a prominent feature or perform a conserved function in other species. The domain itself forms part of the DNA-binding domain. Basic residues on the alpha-1 helix are thought to be important for DNA interaction [1].	Domain
K [auth M], L [auth W]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
K [auth M], L [auth W]	PF00176	SNF2-related domain (SNF2-rel_dom)	SNF2-related domain	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as w ...	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1)[1,2,3]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.	Domain
K [auth M], L [auth W]	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Histone H3	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, F	Histone H4	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	Histone H2A type 1	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D, H	Histone H4	-	-	-
G	Histone H2A type 1	DNA binding binding organic cyclic compound 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 chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
I	DNA (176-MER)	-	-	-
J	DNA (177-MER)	-	-	-
K [auth M], L [auth W]	Chromo domain-containing protein 1	catalytic activity, acting on a nucleic acid helicase 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 organic cyclic compound binding nucleic acid binding catalytic activity, acting on a nucleic acid helicase 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 organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein-containing complex 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 methylated histone binding modification-dependent protein binding methylation-dependent protein binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA-templated transcription DNA-templated transcriptional start site selection regulation of DNA-templated transcription initiation regulation of RNA metabolic process organic substance metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA-templated transcription DNA-templated transcriptional start site selection regulation of DNA-templated transcription initiation regulation of RNA metabolic process organic substance metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process 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 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 DNA-templated transcription initiation regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process transcriptional start site selection at RNA polymerase II promoter metabolic process cellular process regulation of transcription initiation by RNA polymerase II regulation of macromolecule biosynthetic process macromolecule metabolic process 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 protein-containing complex organization protein-DNA complex organization chromatin organization transcription by RNA polymerase I termination of RNA polymerase I transcription 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 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 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 chromatin remodeling nucleosome organization	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex protein-DNA complex chromatin chromosome transferase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex protein-DNA complex chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular non-membrane-bounded organelle protein acetyltransferase complex SAGA-type complex SLIK (SAGA-like) complex intracellular protein-containing complex non-membrane-bounded organelle nucleolar chromatin nucleus membrane-enclosed lumen nuclear chromosome nucleolus intracellular organelle lumen organelle lumen nuclear lumen peptidase complex SAGA complex

InterPro: Protein Family Classification InterPro Database Homepage

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