5M5G

Crystal structure of the Chaetomium Thermophilum polycomb repressive complex 2 (PRC2)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00400	e5m5gA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
A	PF22038	e5m5gA2	A: a/b three-layered sandwiches	X: Polycomb protein Eed insertion domain (From Topology)	H: Polycomb protein Eed insertion domain (From Topology)	T: Polycomb protein Eed insertion domain	F: PF22038	ECOD (1.6)
B	PF00856	e5m5gB7	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)
B	F_UNCLASSIFIED	e5m5gB2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF09733	e5m5gB9	A: alpha arrays	X: lambda integrase-N-like	H: VEFS domain (From Topology)	T: VEFS domain	F: PF09733	ECOD (1.6)
B	PF18264	e5m5gB1	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: PF18264	ECOD (1.6)
B	PF21509	e5m5gB3	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: PF21509	ECOD (1.6)
B	PF18600	e5m5gB5	A: few secondary structure elements	X: Ezh2 MCSS domain (From Topology)	H: Ezh2 MCSS domain (From Topology)	T: Ezh2 MCSS domain	F: PF18600	ECOD (1.6)
B	PF18601	e5m5gB6	A: extended segments	X: Ezh2 N-terminal domain (From Topology)	H: Ezh2 N-terminal domain (From Topology)	T: Ezh2 N-terminal domain	F: PF18601	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B	PF00856	SET domain (SET)	SET domain	-	Family
B	PF21509	Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain (Ezh2-like__CXC_fung)	Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain	This domain is found in a group of mostly fungal proteins, including the Polycomb repressive complex 2 (PRC2) subunit Ezh2 from Chaetomium thermophilum (Swiss:G0SDW4), which is responsible for methylation of histone H3 lysine 27 (H3K27) and therefore ...	This domain is found in a group of mostly fungal proteins, including the Polycomb repressive complex 2 (PRC2) subunit Ezh2 from Chaetomium thermophilum (Swiss:G0SDW4), which is responsible for methylation of histone H3 lysine 27 (H3K27) and therefore involved in epigenetic gene silencing. This entry represents the domain found N-terminal to to the SET domain (Pfam:PF00856). It contains a Zn3Cys8His and a Zn3Cys9 cluster [1-4].	Domain
B	PF18601	EZH2 N-terminal domain (EZH2_N)	EZH2 N-terminal domain	Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 ...	Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. This is the N-terminal domain of EZH2 [1].	Domain
B	PF18600	Fungal MCSS domain (Ezh2_MCSS_fung)	Fungal MCSS domain	Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 ...	Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. The middle lobe largely comprises two domains that mark the beginning of the carboxy (C)-terminal region of EZH2 (MCSS and SANT2) and the helical, C-terminal, component of the Suz12 Vefs domain. This entry describes the MCSS (also known as SANT2L) domain. There is one zinc binding (Zn1Cys3His1) which is formed solely by MCSS [1, 2].	Domain
C [auth D]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	putative polycomb protein EED	-	-	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
B	Putative uncharacterized protein	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity cation binding ion binding binding metal ion binding small molecule binding	methylation metabolic process	-
C [auth D]	HISTONE H3 11-Mer peptide	DNA binding binding organic cyclic compound 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 protein-DNA complex organization cellular component 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 organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	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 protein-DNA complex 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 protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D [auth E]	Fragment from molecular 2 (region containing putative polycomb protein Suz12)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001680	WD40 repeat	Repeat
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR040968	Ezh2, MCSS domain, fungal	Domain
B	IPR046341	SET domain superfamily	Homologous Superfamily
B	IPR048360	Ezh2-like, preSET CXC domain, fungi	Domain
B	IPR040595	EZH2, N-terminal domain	Domain
B	IPR045318	Histone-lysine N-methyltransferase EZH1/2-like	Family
B	IPR001214	SET domain	Domain
B	IPR026489	CXC domain	Domain
C [auth D]	IPR009072	Histone-fold	Homologous Superfamily
C [auth D]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth D]	IPR000164	Histone H3/CENP-A	Family
D [auth E]	IPR019135	Polycomb protein, VEFS-Box	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D]	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth D]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.