2LKM | pdb_00002lkm

Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MRG binding domain-like	8092806	3002625	SCOP2B (2022-06-29)
B	SCOP2 Family	MRG domain-like	8047498	4005668	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	MRG domain-like	8092775	3002620	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	MRG	e2lkmB1	A: alpha arrays	X: MRG domain (From Topology)	H: MRG domain (From Topology)	T: MRG domain	F: MRG	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.5.220	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.274.30	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16737	PHD finger protein 12 MRG binding domain (PHF12_MRG_bd)	PHD finger protein 12 MRG binding domain	This domain found in PHD finger protein 12 binds to the MRG domain of Mortality factor 4-like protein 1 [1].	Domain
B	PF05712	MRG (MRG)	MRG	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PHD finger protein 12	binding phospholipid binding lipid binding phosphatidylinositol binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding cation binding binding phospholipid binding lipid binding phosphatidylinositol binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen transcription regulator complex transcription repressor complex
B	Mortality factor 4-like protein 1	chromatin binding binding	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 fibroblast proliferation cell population proliferation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death cell cycle regulation of cell cycle cellular component organization chromatin organization cellular component organization or biogenesis	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 Sin3-type complex nuclear protein-containing complex nuclear chromosome histone deacetylase complex protein-DNA complex nucleosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR000253	Forkhead-associated (FHA) domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR031966	PHD finger protein 12, MRG binding domain	Domain
A	IPR038098	PHD finger protein 12, MRG binding domain superfamily	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR042163	PHD finger protein 12	Family
B	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
B	IPR025995	RNA binding activity-knot of a chromodomain	Domain
B	IPR008676	MRG	Family
B	IPR026541	MRG domain	Domain
B	IPR038217	MRG, C-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96QT6	acute myeloid leukemia endogenous depression large cell medulloblastoma ovarian cancer atypical teratoid rhabdoid tumor glioblastoma medulloblastoma primitive neuroectodermal tumor bipolar disorder juvenile dermatomyositis osteosarcoma
B	Pharos: Q9UBU8	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma lung carcinoma skin basal cell carcinoma heart disease myocardial infarction small cell lung carcinoma lung adenocarcinoma squamous cell lung carcinoma

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.