6ZHY | pdb_00006zhy

Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8041272	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)
D	Histone	e6zhyD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
C	Histone_1	e6zhyC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
F	Histone_1	e6zhyF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
B	Histone_1	e6zhyB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
A	Histone	e6zhyA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e6zhyE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth K]	Chromodomain-helicase-DNA-binding protein 1-like	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity macromolecular conformation isomerase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity macromolecular conformation isomerase activity ATP-dependent activity ATP-dependent chromatin remodeler activity adenyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding ADP-D-ribose modification-dependent protein binding poly-ADP-D-ribose modification-dependent protein binding protein binding modification-dependent protein binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity 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 protein-containing complex binding chromatin binding nucleosome binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair cellular component organization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome
H [auth J]	DNA (110-MER) Widom 601 sequence	-	-	-
G [auth I]	DNA (110-MER) Widom 601 sequence	-	-	-
D	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
C	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
B, 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
A, E	Histone H3	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth K]	IPR000330	SNF2, N-terminal	Domain
I [auth K]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
I [auth K]	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
I [auth K]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
I [auth K]	IPR031053	Chromodomain-helicase-DNA-binding protein 1-like	Family
I [auth K]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
I [auth K]	IPR002589	Macro domain	Domain
I [auth K]	IPR001650	Helicase, C-terminal domain-like	Domain
I [auth K]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
I [auth K]	IPR043472	Macro domain-like	Homologous Superfamily
D	IPR009072	Histone-fold	Homologous Superfamily
D	IPR055333	Histone H2B, conserved site	Conserved Site
D	IPR000558	Histone H2B	Family
D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C	IPR009072	Histone-fold	Homologous Superfamily
C	IPR002119	Histone H2A	Family
C	IPR032454	Histone H2A, C-terminal domain	Domain
C	IPR032458	Histone H2A conserved site	Conserved Site
C	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
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
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR000164	Histone H3/CENP-A	Family
A, E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth K]	Pharos: Q86WJ1	substance dependence Substance-Related Disorders astrocytic tumor congenital anomaly of kidney and urinary tract lung cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia substance abuse thrombocytopenia-absent radius syndrome atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma substance-related disorder chromosome 1q21.1 deletion syndrome drug dependence large cell medulloblastoma substance dependence Substance-Related Disorders astrocytic tumor congenital anomaly of kidney and urinary tract lung cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia substance abuse thrombocytopenia-absent radius syndrome atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma substance-related disorder chromosome 1q21.1 deletion syndrome drug dependence large cell medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis