2XD7

Crystal structure of the macro domain of human core histone H2A

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)
A	d2xd7a_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2xd7b_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2xd7c_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2xd7d_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	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)
A	SCOP2B Superfamily	Macro domain-like	8067144	3000458	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Macro domain-like	8067144	3000458	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Macro domain-like	8067144	3000458	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Macro domain-like	8067144	3000458	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	Macro	e2xd7A1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
B	Macro	e2xd7B1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
C	Macro	e2xd7C1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
D	Macro	e2xd7D1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
B	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
C	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
D	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01661	Macro domain (Macro)	Macro domain	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CORE HISTONE MACRO-H2A.2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin RNA polymerase II transcription regulatory region sequence-specific DNA binding chromatin binding chromatin DNA binding protein-containing complex binding nucleosome binding nucleosomal DNA binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process cellular component organization 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 epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation 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 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 cellular process macromolecule metabolic process regulation of metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component biogenesis cellular component assembly protein-containing complex assembly nucleosome assembly nucleosome organization sex-chromosome dosage compensation heterochromatin formation positive regulation of keratinocyte differentiation cellular developmental process regulation of developmental process regulation of epidermal cell differentiation epidermis development positive regulation of biological process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of cellular process epithelium development regulation of multicellular organismal development epidermal cell differentiation positive regulation of epidermis development tissue development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation positive regulation of multicellular organismal process regulation of epidermis development regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process negative regulation of transcription of nucleolar large rRNA by RNA polymerase I transcription by RNA polymerase I rRNA transcription regulation of transcription by RNA polymerase I regulation of transcription of nucleolar large rRNA by RNA polymerase I negative regulation of transcription by RNA polymerase I rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I protein localization establishment of protein localization cellular localization protein localization to chromatin establishment of protein localization to chromatin establishment of localization localization establishment of protein localization to organelle protein localization to chromosome cellular macromolecule localization macromolecule localization protein localization to organelle establishment of protein localization to chromosome	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 protein-DNA complex nucleosome 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 protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle 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 chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035796	Core histone macro-H2A, macro domain	Domain
A, B, C, D	IPR002119	Histone H2A	Family
A, B, C, D	IPR021171	Core histone macro-H2A	Family
A, B, C, D	IPR032454	Histone H2A, C-terminal domain	Domain
A, B, C, D	IPR009072	Histone-fold	Homologous Superfamily
A, B, C, D	IPR007125	Histone H2A/H2B/H3	Domain
A, B, C, D	IPR002589	Macro domain	Domain
A, B, C, D	IPR043472	Macro domain-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9P0M6	atypical teratoid rhabdoid tumor medulloblastoma large cell medulloblastoma osteosarcoma lung carcinoma primitive neuroectodermal tumor

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.