5FUG | pdb_00005fug

Crystal structure of a human YL1-H2A.Z-H2B 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)
K	d5fugk_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5fugh_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5fuge_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5fugb_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5fugj_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5fugg_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5fugd_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fuga_	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)
L	SCOP2 Family	YL1-Z domain-like	8047553	4005691	SCOP2 (2022-06-29)
L	SCOP2 Superfamily	YL1-Z domain-like	8093147	3002684	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	YL1-Z domain-like	8093147	3002684	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YL1-Z domain-like	8093147	3002684	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YL1-Z domain-like	8093147	3002684	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Core histone-like	8036779	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8036779	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8036779	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)
K	Histone	e5fugK1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e5fugH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e5fugE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B	Histone	e5fugB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
J	Histone_1	e5fugJ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
G	Histone_1	e5fugG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
D	Histone_1	e5fugD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
A	Histone_1	e5fugA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
H	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
E	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)
J	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
G	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
D	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, D, G, J	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, D, G, J	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
C, F, I, L	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG	DNA binding binding nucleic acid binding protein binding histone binding protein carrier chaperone histone chaperone activity molecular carrier activity	cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process DNA repair positive regulation of DNA recombination double-strand break repair regulation of biological process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process DNA damage response regulation of response to stimulus metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process multicellular organismal process somatic stem cell population maintenance maintenance of cell number stem cell population maintenance regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death cell cycle regulation of cell cycle negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure protein-containing complex intracellular anatomical structure catalytic complex NuA4 histone acetyltransferase complex intracellular membraneless organelle chromatin chromosome transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein-DNA complex nucleosome
B, E, H, K	HISTONE H2B TYPE 1-J	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity lipid binding lipopolysaccharide binding carbohydrate derivative 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 biological process involved in interspecies interaction between organisms 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 biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus 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 disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to Gram-negative bacterium defense response to bacterium response to bacterium antibacterial humoral response 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 cellular response to stimulus regulation of cellular process negative regulation of signaling signaling negative regulation of biological process response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor negative regulation of cellular process tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway biological regulation negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor defense response to Gram-positive bacterium	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex 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 organelle membraneless organelle chromosome, centromeric region extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, D, G, J	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	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 extracellular space vesicle extracellular membrane-bounded organelle euchromatin protein-containing complex protein-DNA complex nucleosome nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR013272	Vps72/YL1, C-terminal	Domain
C, F, I, L	IPR046757	Vps72/YL1, N-terminal	Domain
B, E, H, K	IPR009072	Histone-fold	Homologous Superfamily
B, E, H, K	IPR000558	Histone H2B	Family
B, E, H, K	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B, E, H, K	IPR055333	Histone H2B, conserved site	Conserved Site
A, D, G, J	IPR009072	Histone-fold	Homologous Superfamily
A, D, G, J	IPR002119	Histone H2A	Family
A, D, G, J	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, D, G, J	IPR032454	Histone H2A, C-terminal domain	Domain
A, D, G, J	IPR032458	Histone H2A conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F, I, L	Pharos: Q15906	acute myeloid leukemia lung cancer medulloblastoma ovarian cancer heart disease malignant mesothelioma myocardial infarction tuberculosis lung adenocarcinoma Malignant neoplasm of breast osteosarcoma
B, E, H, K	Pharos: P06899	autism spectrum disorder lung adenocarcinoma breast cancer schizophrenia endogenous depression
A, D, G, J	Pharos: P0C0S5	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

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.