7CJ0

Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth E]	d7cj0e_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d7cj0b_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth C]	d7cj0c_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth F]	d7cj0f_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth C]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	MCM2 histone-binding domains (HBDs)	8107353	3002871	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	MCM2 histone-binding domains (HBDs)	8107353	3002871	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 [auth E]	Histone	e7cj0E1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E [auth B]	Histone	e7cj0B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
F [auth C]	Histone_1	e7cj0C1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
B [auth F]	Histone_1	e7cj0F1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth F], F [auth C]	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 E], E [auth B]	Histone H3.3	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process cellular developmental process ossification cell differentiation osteoblast differentiation cell population proliferation cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process pericentric heterochromatin formation regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation 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 sexual reproduction fertilization single fertilization regulation of centromere complex assembly protein-containing complex organization chromosome organization protein-DNA complex assembly regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization cellular component biogenesis protein-DNA complex organization organelle organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly centromere complex assembly multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation female gamete generation gamete generation oocyte development anatomical structure maturation germ cell development oocyte maturation oocyte differentiation cell maturation nucleosome assembly nucleosome organization spermatid development spermatid differentiation spermatogenesis male gamete generation negative regulation of cellular component organization regulation of chromosome condensation negative regulation of chromosome condensation negative regulation of chromosome organization negative regulation of organelle organization chromosome condensation subtelomeric heterochromatin formation telomere organization muscle structure development muscle cell differentiation nucleus organization multicellular organism growth developmental growth	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure chromosome chromosomal region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure chromosome chromosomal region kinetochore intracellular organelle intracellular non-membrane-bounded organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome non-membrane-bounded organelle protein-DNA complex nucleosome chromatin sex chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen Barr body nuclear lumen X chromosome nucleoplasm chromosome, telomeric region
B [auth F], F [auth C]	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding 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 organelle organization 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 organelle organization telomere organization chromosome organization protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C [auth G], G [auth H]	DNA replication licensing factor MCM2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding histone binding 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 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 enzyme binding cation binding metal ion binding single-stranded DNA binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication DNA replication initiation response to interleukin-4 response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 cellular process apoptotic process cell death programmed cell death regulation of DNA-templated DNA replication initiation regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process cellular response to stimulus double-strand break repair DNA recombination double-strand break repair via break-induced replication cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair 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 component organization or biogenesis nucleosome assembly nucleosome organization mitotic DNA replication cell cycle DNA replication initiation nuclear DNA replication cell cycle DNA replication mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cell cycle cell cycle process DNA duplex unwinding DNA geometric change chromosome organization DNA conformation change DNA unwinding involved in DNA replication organelle organization	membrane-bounded organelle DNA replication preinitiation complex protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle membrane-bounded organelle DNA replication preinitiation complex protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle intracellular non-membrane-bounded organelle CMG complex nuclear lumen non-membrane-bounded organelle cytoplasm MCM complex chromatin nuclear origin of replication recognition complex origin recognition complex chromosome, telomeric region chromosomal region
D, H [auth A]	DnaJ homolog subfamily C member 9	protein binding binding histone binding heat shock protein binding protein-folding chaperone binding	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 positive regulation of molecular function 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 positive regulation of molecular function regulation of molecular function regulation of ATP-dependent activity positive regulation of ATP-dependent activity biological regulation	protein-containing complex protein folding chaperone complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane extracellular region extracellular space membrane-bounded organelle nucleus protein-containing complex protein folding chaperone complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], E [auth B]	IPR000164	Histone H3/CENP-A	Family
A [auth E], E [auth B]	IPR009072	Histone-fold	Homologous Superfamily
A [auth E], E [auth B]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth F], F [auth C]	IPR009072	Histone-fold	Homologous Superfamily
B [auth F], F [auth C]	IPR035425	CENP-T/Histone H4, histone fold	Domain
B [auth F], F [auth C]	IPR001951	Histone H4	Family
B [auth F], F [auth C]	IPR019809	Histone H4, conserved site	Conserved Site
B [auth F], F [auth C]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C [auth G], G [auth H]	IPR031327	Mini-chromosome maintenance protein	Family
C [auth G], G [auth H]	IPR018525	Mini-chromosome maintenance, conserved site	Conserved Site
C [auth G], G [auth H]	IPR001208	MCM domain	Domain
C [auth G], G [auth H]	IPR041562	MCM, AAA-lid domain	Domain
C [auth G], G [auth H]	IPR008045	DNA replication licensing factor Mcm2	Family
C [auth G], G [auth H]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth G], G [auth H]	IPR027925	MCM, N-terminal domain	Domain
C [auth G], G [auth H]	IPR033762	MCM OB domain	Domain
C [auth G], G [auth H]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
D, H [auth A]	IPR018253	DnaJ domain, conserved site	Conserved Site
D, H [auth A]	IPR052594	J domain-containing protein	Family
D, H [auth A]	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
D, H [auth A]	IPR001623	DnaJ domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth E], E [auth B]	Pharos: P84243	malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial intellectual disability lung cancer malignant mesothelioma pituitary cancer atopic eczema subependymal giant cell astrocytoma breast cancer cutaneous lupus erythematosus glioma susceptibility 1 invasive ductal breast carcinoma malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma plasma cell myeloma atypical teratoid rhabdoid tumor subependymoma breast carcinoma Down syndrome exocrine pancreatic carcinoma hepatocellular carcinoma
B [auth F], F [auth C]	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma allergic rhinitis ulcerative colitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
C [auth G], G [auth H]	Pharos: P49736	autosomal dominant nonsyndromic deafness 70 malignant colon neoplasm nonsyndromic genetic deafness nasopharyngeal carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma colonic neoplasm glioblastoma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer pituitary cancer autosomal dominant nonsyndromic deafness 70 malignant colon neoplasm nonsyndromic genetic deafness nasopharyngeal carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma colonic neoplasm glioblastoma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer pituitary cancer Sensorineural hearing loss, bilateral atypical teratoid rhabdoid tumor benign colon neoplasm ductal breast carcinoma in situ hepatocellular carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor autosomal dominant nonsyndromic deafness 1 breast cancer endometriosis invasive ductal breast carcinoma lung cancer malignant glioma