3R93

Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3r93a_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3r93b_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3r93c_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3r93d_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	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	Chromo domain-like	8066167	3000161	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Chromo domain-like	8066167	3000161	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Chromo domain-like	8066167	3000161	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Chromo domain-like	8066167	3000161	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	PF00385	e3r93A1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF00385	ECOD (1.6)
B	PF00385	e3r93B1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF00385	ECOD (1.6)
C	PF00385	e3r93C1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF00385	ECOD (1.6)
D	PF00385	e3r93D1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF00385	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain	-	Domain
E, F, G, H	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, B, C, D	M-phase phosphoprotein 8	histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding chromatin binding binding methylated histone binding protein binding modification-dependent protein binding histone binding methylation-dependent protein binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 protein-containing complex organization 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 positive regulation of organelle organization cellular component biogenesis regulation of heterochromatin formation regulation of chromatin organization regulation of DNA methylation-dependent heterochromatin formation regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of DNA methylation-dependent heterochromatin formation positive regulation of heterochromatin formation DNA methylation-dependent heterochromatin formation positive regulation of chromatin organization positive regulation of cellular process heterochromatin formation positive regulation of cellular component biogenesis chromosome organization regulation of cellular component biogenesis organelle organization facultative heterochromatin formation viral life cycle negative regulation of RNA biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process primary metabolic process single stranded viral RNA replication via double stranded DNA intermediate organic cyclic compound metabolic process viral genome replication organic cyclic compound biosynthetic process negative regulation of RNA metabolic process regulation of single stranded viral RNA replication via double stranded DNA intermediate RNA metabolic process negative regulation of single stranded viral RNA replication via double stranded DNA intermediate RNA biosynthetic process nucleic acid biosynthetic process negative regulation of viral process viral RNA genome replication viral process regulation of RNA biosynthetic process negative regulation of viral genome replication nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of viral process regulation of viral life cycle regulation of viral genome replication	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex protein-DNA complex chromatin chromosome heterochromatin cytoplasm cytosol cell periphery plasma membrane membrane nucleosome nucleoplasm
E, F, G, H	H3K9Me3 peptide	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding 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	extracellular region cellular anatomical entity 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 extracellular region cellular anatomical entity 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002110	Ankyrin repeat	Repeat
A, B, C, D	IPR000953	Chromo/chromo shadow domain	Domain
A, B, C, D	IPR023780	Chromo domain	Domain
A, B, C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR023779	Chromo domain, conserved site	Conserved Site
E, F, G, H	IPR009072	Histone-fold	Homologous Superfamily
E, F, G, H	IPR007125	Histone H2A/H2B/H3	Domain
E, F, G, H	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q99549	adenoma osteosarcoma glioblastoma ovarian cancer malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
E, F, G, H	Pharos: Q71DI3	idiopathic scoliosis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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 R01GM133198.