4NFT | pdb_00004nft

Crystal structure of human lnkH2B-h2A.Z-Anp32e

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)
D	d4nftd1	All alpha proteins	Histone-fold	Histone-fold	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4nftc1	All alpha proteins	Histone-fold	Histone-fold	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4nftb1	All alpha proteins	Histone-fold	Histone-fold	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4nftb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4nfta1	All alpha proteins	Histone-fold	Histone-fold	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4nfta3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ], 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)
D	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8036779	3001387	SCOP2B (2022-06-29)
C	SCOP2 Family	Nucleosome core histones	8066282	4000793	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Core histone-like	8066283	3001387	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8036779	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8036779	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8036779	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	FeoB_N	e4nftD1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: FeoB_N	ECOD (v294.1)
C	FeoB_N	e4nftC1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: FeoB_N	ECOD (v294.1)
B	HypA	e4nftB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: HypA	ECOD (v294.1)
A		e4nftA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
C	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
B	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, B, C, D	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
E, F	Acidic leucine-rich nuclear phosphoprotein 32 family member E	protein binding binding histone binding enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity enzyme inhibitor activity protein folding chaperone histone chaperone activity protein carrier activity molecular carrier activity	regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death cellular component organization chromatin organization cellular component organization or biogenesis	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle ATPase complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen histone deacetylase complex nucleoplasm membraneless organelle SWI/SNF superfamily-type complex INO80-type complex catalytic complex intracellular membraneless organelle chromatin Swr1 complex organelle lumen nuclear lumen transport vesicle membrane endomembrane system presynapse bounding membrane of organelle vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle organelle membrane exocytic vesicle endosome membrane postsynaptic endosome endosome postsynaptic endosome membrane glutamatergic synapse
A, B, C, D	Histone H2B type 2-E, Histone H2A.Z	DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding protein-containing complex binding nucleosome binding nucleosomal DNA binding sequence-specific DNA binding double-stranded DNA 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 DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding protein-containing complex binding nucleosome binding nucleosomal DNA binding sequence-specific DNA binding double-stranded DNA 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding 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 cellular response to stimulus response to lipid response to stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to estradiol cellular response to estradiol stimulus 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 nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization biological process involved in interspecies interaction between organisms innate immune response in mucosa immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antibacterial humoral response defense response to bacterium response to bacterium defense response to Gram-positive bacterium	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle euchromatin protein-containing complex protein-DNA complex nucleosome nucleus intracellular membrane-bounded organelle cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR001611	Leucine-rich repeat	Repeat
E, F	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
E, F	IPR045081	Acidic leucine-rich nuclear phosphoprotein 32	Family
A, B, C, D	IPR009072	Histone-fold	Homologous Superfamily
A, B, C, D	IPR002119	Histone H2A	Family
A, B, C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B, C, D	IPR032454	Histone H2A, C-terminal domain	Domain
A, B, C, D	IPR032458	Histone H2A conserved site	Conserved Site
A, B, C, D	IPR009072	Histone-fold	Homologous Superfamily
A, B, C, D	IPR000558	Histone H2B	Family
A, B, C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B, C, D	IPR055333	Histone H2B, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: Q9BTT0	atopic eczema ovarian cancer psoriasis amyotrophic lateral sclerosis bipolar disorder cutaneous lupus erythematosus gastric carcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer dermatomyositis glioblastoma atopic eczema ovarian cancer psoriasis amyotrophic lateral sclerosis bipolar disorder cutaneous lupus erythematosus gastric carcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer dermatomyositis glioblastoma lung adenocarcinoma malignant colon neoplasm non-small cell lung carcinoma plasma cell myeloma atypical teratoid rhabdoid tumor Crohn disease ductal breast carcinoma in situ invasive ductal breast carcinoma lung cancer malignant mesothelioma
A, B, C, D	Pharos: Q16778	adrenal cortex carcinoma dermatomyositis endometriosis lung cancer ovarian cancer psoriasis breast cancer diabetes mellitus IgA glomerulonephritis lymphoplasmacytic lymphoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma ductal breast carcinoma in situ invasive ductal breast carcinoma medulloblastoma adrenal cortex carcinoma dermatomyositis endometriosis lung cancer ovarian cancer psoriasis breast cancer diabetes mellitus IgA glomerulonephritis lymphoplasmacytic lymphoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma ductal breast carcinoma in situ invasive ductal breast carcinoma medulloblastoma plasma cell myeloma breast carcinoma spina bifida breast cancer cystic fibrosis invasive ductal breast carcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma ductal breast carcinoma in situ lung carcinoma medulloblastoma ovarian cancer pilocytic astrocytoma psoriasis cancer idiopathic scoliosis malignant colon neoplasm nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer

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.