3OB9 | pdb_00003ob9

Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution

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)
E	d3ob9e_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ob9d1	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ob9d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ob9c_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ob9b_	All beta proteins	SH3-like barrel	Chromo domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ob9a_	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)
E	SCOP2B Superfamily	Chromo domain-like	8089216	3000161	SCOP2B (2022-06-29)
D	SCOP2 Family	Chromo barrel domain	8089215	4003139	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Chromo domain-like	8089216	3000161	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Chromo domain-like	8089216	3000161	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Chromo domain-like	8089216	3000161	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Chromo domain-like	8089216	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)
E	Tudor-knot_1	e3ob9E1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Tudor-knot_1	ECOD (1.6)
D	Tudor-knot_1	e3ob9D1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Tudor-knot_1	ECOD (1.6)
C	Tudor-knot_1	e3ob9C1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Tudor-knot_1	ECOD (1.6)
B	Tudor-knot_1	e3ob9B1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Tudor-knot_1	ECOD (1.6)
A	Tudor-knot_1	e3ob9A1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Tudor-knot_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF11717	RNA binding activity-knot of a chromodomain (Tudor-knot)	RNA binding activity-knot of a chromodomain	-	Family
A, B, C, D, E	PF22732	MSL3 chromodomain-like (MSL3_chromo-like)	MSL3 chromodomain-like	This domain is found in Male-specific lethal-3 (MSL3) and other related proteins such as MRG15 transcription factor. MSL3 resides in the MSL (male-specific lethal) complex, which upregulates transcription by spreading the histone H4 Lys16 acetyl mark ...	This domain is found in Male-specific lethal-3 (MSL3) and other related proteins such as MRG15 transcription factor. MSL3 resides in the MSL (male-specific lethal) complex, which upregulates transcription by spreading the histone H4 Lys16 acetyl mark. The MSL3 chromo domain implicated in chromatin targeting and its deletion leads to the disruption of MSL targeting. The MRG15 chromo domain is involved in chromatin remodelling and transcription regulation. This domain consists of a SH3-like beta-barrel and a long alpha-helix.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Male-specific lethal 3-like 1 (Drosophila), isoform CRA_c	DNA binding binding nucleic acid binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone H4K16ac reader activity histone H4 reader activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex MSL complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex MSL complex acetyltransferase complex H4 histone acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex NuA4 histone acetyltransferase complex H4/H2A histone acetyltransferase complex 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, E	IPR000953	Chromo/chromo shadow domain	Domain
A, B, C, D, E	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR053820	MSL3 chromodomain-like	Domain
A, B, C, D, E	IPR008676	MRG	Family
A, B, C, D, E	IPR026541	MRG domain	Domain
A, B, C, D, E	IPR038217	MRG, C-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: Q8N5Y2	breast cancer Facies gastric carcinoma large cell medulloblastoma ovarian cancer psoriasis glioblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma X-linked disease developmental disability gastric cancer intellectual disability osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

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.