7XYG

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome

External Resource: Annotation

Domain Annotation: SCOP2 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 [auth C]	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2021-05-27)
B [auth G]	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2021-05-27)
C [auth D]	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2021-05-27)
D [auth H]	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2021-05-27)
H [auth A]	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2021-05-27)
I [auth E]	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2021-05-27)
J [auth B]	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2021-05-27)
K [auth F]	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth G]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
G [auth K]	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
G [auth K]	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
J [auth B], K [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth G]	Histone H2A	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 heterochromatin organization protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 heterochromatin organization developmental process muscle structure development multicellular organism development multicellular organismal process somatic muscle development larval somatic muscle development anatomical structure development larval development post-embryonic development	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth D], D [auth H]	Histone H2B	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity protein-containing complex binding structural molecule activity structural constituent of chromatin	protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process cellular component organization or biogenesis	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
E [auth J]	DNA (167-MER)	-	-	-
F [auth I]	DNA (167-MER)	-	-	-
G [auth K]	ATP-dependent helicase fft3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity catalytic activity, acting on DNA protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity protein-containing complex binding chromatin 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 damaged DNA binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process replication fork processing nucleic acid metabolic process transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process protein-DNA complex organization nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process replication fork processing nucleic acid metabolic process transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling protein-containing complex organization cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription elongation biosynthetic process cellular process attachment of telomeric heterochromatin to nuclear envelope localization chromosome localization organelle localization chromosome attachment to the nuclear envelope cell cycle cell cycle process	protein-containing complex intracellular anatomical structure protein-DNA complex chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
H [auth A], I [auth E]	Histone H3	DNA binding protein-containing complex binding binding chromatin binding organic cyclic compound binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex protein-DNA complex nucleosome chromatin
J [auth B], K [auth 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 organization protein-DNA complex assembly protein-DNA complex organization cellular component 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex nuclear protein-containing complex RCAF complex protein-DNA complex nucleosome chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth G]	IPR009072	Histone-fold	Homologous Superfamily
A [auth C], B [auth G]	IPR007125	Histone H2A/H2B/H3	Domain
A [auth C], B [auth G]	IPR002119	Histone H2A	Family
A [auth C], B [auth G]	IPR032454	Histone H2A, C-terminal domain	Domain
A [auth C], B [auth G]	IPR032458	Histone H2A conserved site	Conserved Site
C [auth D], D [auth H]	IPR009072	Histone-fold	Homologous Superfamily
C [auth D], D [auth H]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth D], D [auth H]	IPR000558	Histone H2B	Family
G [auth K]	IPR000330	SNF2, N-terminal	Domain
G [auth K]	IPR001650	Helicase, C-terminal domain-like	Domain
G [auth K]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
G [auth K]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
G [auth K]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
G [auth K]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
H [auth A], I [auth E]	IPR009072	Histone-fold	Homologous Superfamily
H [auth A], I [auth E]	IPR007125	Histone H2A/H2B/H3	Domain
H [auth A], I [auth E]	IPR000164	Histone H3/CENP-A	Family
J [auth B], K [auth F]	IPR009072	Histone-fold	Homologous Superfamily
J [auth B], K [auth F]	IPR035425	CENP-T/Histone H4, histone fold	Domain
J [auth B], K [auth F]	IPR001951	Histone H4	Family
J [auth B], K [auth F]	IPR019809	Histone H4, conserved site	Conserved Site
J [auth B], K [auth F]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold 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 R01GM133198.

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7XYG

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage