6TEM | pdb_00006tem

CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8041279	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)
E	SCOP2B Superfamily	Core histone-like	8070539	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8070539	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	NADH_4Fe-4S	e6temC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: NADH_4Fe-4S	ECOD (v294.1)
G	Cation_ATPase_C,Cation_ATPase_N	e6temG1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v294.1)
H	Cation_ATPase_C,Cation_ATPase_N	e6temH1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v294.1)
D	NADH_4Fe-4S	e6temD1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: NADH_4Fe-4S	ECOD (v294.1)
F	Cation_ATPase_C,Cation_ATPase_N	e6temF1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v294.1)
B	NADH_4Fe-4S	e6temB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: NADH_4Fe-4S	ECOD (v294.1)
E	NADH_4Fe-4S	e6temE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: NADH_4Fe-4S	ECOD (v294.1)
A	Cation_ATPase_C,Cation_ATPase_N	e6temA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
G	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
H	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
D	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
F	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
B	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
E	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, G	Histone H2A	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
J	Widom 601 DNA (145-MER, antisense)	-	-	-
I	Widom 601 DNA (145-MER, sense)	-	-	-
D, 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
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-like centromeric protein A	DNA binding binding nucleic acid binding chromatin binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly CENP-A containing chromatin assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly chromatin organization kinetochore assembly protein-containing complex assembly kinetochore organization cellular process organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly CENP-A containing chromatin assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly chromatin organization kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis establishment of organelle localization cellular localization microtubule cytoskeleton organization spindle localization establishment or maintenance of cell polarity mitotic cell cycle localization establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation organelle localization establishment of localization in cell cell cycle microtubule cytoskeleton organization involved in mitosis cell cycle process establishment of localization establishment of cell polarity mitotic cell cycle process establishment of mitotic spindle orientation microtubule-based process cytoskeleton organization cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division protein localization to chromosome, centromeric region protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization protein localization to chromatin protein localization to CENP-A containing chromatin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region condensed chromosome, centromeric region condensed chromosome protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region condensed chromosome, centromeric region condensed chromosome protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromatin chromosome, centromeric core domain CENP-A containing nucleosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
D, H	IPR000558	Histone H2B	Family
D, H	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	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, E	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, E	Pharos: P49450	medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis adrenal cortex carcinoma breast cancer endometriosis hypertensive disorder large cell medulloblastoma malignant colon neoplasm malignant mesothelioma nasopharyngeal carcinoma ovarian cancer primitive neuroectodermal tumor atopic eczema medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis adrenal cortex carcinoma breast cancer endometriosis hypertensive disorder large cell medulloblastoma malignant colon neoplasm malignant mesothelioma nasopharyngeal carcinoma ovarian cancer primitive neuroectodermal tumor atopic eczema breast carcinoma glioblastoma IgA glomerulonephritis lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma lung cancer malignant glioma

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.