9LRV | pdb_00009lrv

Cryo-EM structure of Fission yeast centromeric nucleosome Class 1

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
E	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone H3-like centromeric protein cnp1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding centromeric DNA binding nucleic acid 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	intracellular organelle chromosome, centromeric core domain cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome, centromeric region chromosome chromosomal region CENP-A containing chromatin chromatin condensed chromosome, centromeric region condensed chromosome intracellular organelle chromosome, centromeric core domain cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome, centromeric region chromosome chromosomal region CENP-A containing chromatin chromatin condensed chromosome, centromeric region condensed chromosome protein-containing complex protein-DNA complex nucleosome CENP-A containing nucleosome 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 chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor 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, G	Histone H2A-alpha	DNA binding binding nucleic acid binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling response to stimulus signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling response to stimulus signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process DNA damage response negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage cellular process negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle organelle fission meiotic cell cycle process nuclear division organelle organization meiosis I meiosis I cell cycle process nuclear chromosome segregation meiotic nuclear division homologous chromosome segregation chromosome segregation mitotic nuclear division mitotic chromosome condensation chromosome organization sister chromatid segregation chromosome condensation mitotic sister chromatid segregation double-strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair	intracellular organelle rDNA heterochromatin cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin mating-type region heterochromatin protein-containing complex protein-DNA complex nucleosome intracellular organelle rDNA heterochromatin cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin mating-type region heterochromatin protein-containing complex protein-DNA complex nucleosome chromosome, subtelomeric region chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle pericentric heterochromatin chromosome, centromeric region
D, H	Histone H2B-alpha	DNA binding binding nucleic acid binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	cellular response to stimulus double-strand break repair response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle site of double-strand break site of DNA damage membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle site of double-strand break site of DNA damage membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E	Histone H3-like centromeric protein cnp1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding centromeric DNA binding nucleic acid 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	intracellular organelle chromosome, centromeric core domain cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome, centromeric region chromosome chromosomal region CENP-A containing chromatin chromatin condensed chromosome, centromeric region condensed chromosome intracellular organelle chromosome, centromeric core domain cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome, centromeric region chromosome chromosomal region CENP-A containing chromatin chromatin condensed chromosome, centromeric region condensed chromosome protein-containing complex protein-DNA complex nucleosome CENP-A containing nucleosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
I	DNA (144-MER)	-	-	-
J	DNA (144-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.