4Z2M | pdb_00004z2m

Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth J]	d4z2mj_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d4z2mh_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth I]	d4z2mi_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth G]	d4z2mg_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	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)
E [auth J]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
B [auth G]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
A [auth B]	SCOP2 Family	Histone chaperone Rttp106-like	8051089	4001923	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	PH domain-like	8103651	3000134	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	PH domain-like	8103657	3000134	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth J]	Histone_1	e4z2mJ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C [auth H]	Histone_1	e4z2mH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
D [auth I]	Histone	e4z2mI1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B [auth G]	Histone	e4z2mG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
A [auth B]	Rtt106	e4z2mB1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: Rtt106	ECOD (1.6)
A [auth B]	SPT16	e4z2mB2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: SPT16	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth J]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
C [auth H]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
D [auth I]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
B [auth G]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A [auth B]	2.30.29.150	Mainly Beta	Roll	PH-domain like		CATH (4.3.0)
A [auth B]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth H], E [auth J]	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
A [auth B]	PF08512	Histone chaperone Rttp106-like, middle domain (Rttp106-like_middle)	Histone chaperone Rttp106-like, middle domain	This Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin tran ...	This Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin transactions) complex subunits, such as Spt16 and either Pob3 (yeast) or the related SSRP1 (higher eukaryotes). This domain plays a role in DNA binding [2-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H], E [auth J]	Histone H4	DNA binding 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 localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development 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 negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth G], D [auth I]	Histone H3.1	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity 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 biosynthetic process 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure membrane 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 protein-DNA complex cellular anatomical structure membrane 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 protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A [auth B]	FACT complex subunit SPT16	RNA binding binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome 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 nucleobase-containing compound metabolic process 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 nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II transcription elongation by RNA polymerase II cellular component disassembly protein-DNA complex disassembly protein-containing complex disassembly nucleosome disassembly	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure FACT complex nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth H], E [auth J]	IPR009072	Histone-fold	Homologous Superfamily
C [auth H], E [auth J]	IPR035425	CENP-T/Histone H4, histone fold	Domain
C [auth H], E [auth J]	IPR001951	Histone H4	Family
C [auth H], E [auth J]	IPR019809	Histone H4, conserved site	Conserved Site
C [auth H], E [auth J]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
B [auth G], D [auth I]	IPR009072	Histone-fold	Homologous Superfamily
B [auth G], D [auth I]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth G], D [auth I]	IPR000164	Histone H3/CENP-A	Family
A [auth B]	IPR033825	FACT complex subunit Spt16, peptidase M24-like domain	Domain
A [auth B]	IPR048969	FACT complex subunit SPT16, C-terminal domain	Domain
A [auth B]	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal	Homologous Superfamily
A [auth B]	IPR011993	PH-like domain superfamily	Homologous Superfamily
A [auth B]	IPR013719	Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain	Domain
A [auth B]	IPR040258	FACT complex subunit Spt16	Family
A [auth B]	IPR013953	FACT complex subunit SPT16, middle domain	Domain
A [auth B]	IPR029148	FACT complex subunit SPT16, N-terminal lobe domain	Domain
A [auth B]	IPR056595	FACT complex subunit SPT16, PH-like domain	Domain
A [auth B]	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A [auth B]	IPR000994	Peptidase M24	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth H], E [auth J]	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
B [auth G], D [auth I]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A [auth B]	Pharos: Q9Y5B9	adenoma glioblastoma malignant glioma osteosarcoma astrocytic tumor large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor malignant ependymoma oligodendroglioma subependymal giant cell astrocytoma

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.