2RJE

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), orthorhombic form II

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	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	PF02820	e2rjeA9	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF02820	ECOD (1.6)
B	PF02820	e2rjeB12	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF02820	ECOD (1.6)
C	PF02820	e2rjeC9	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF02820	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C	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	PF02820	mbt repeat (MBT)	mbt repeat	The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein Swiss:Q9VHA0. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved g ...	The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein Swiss:Q9VHA0. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function.	Domain
D [auth P], E [auth Q]	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Lethal(3)malignant brain tumor-like protein	protein binding binding histone binding SAM domain binding protein domain specific binding protein-containing complex binding chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding methylated histone binding protein binding binding histone binding SAM domain binding protein domain specific binding protein-containing complex binding chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding methylated histone binding modification-dependent protein binding methylation-dependent protein binding identical protein binding nucleosome binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic mitotic nuclear division regulation of cellular component organization regulation of cell cycle process organelle fission regulation of mitotic nuclear division regulation of organelle organization mitotic cell cycle regulation of mitotic cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division cell cycle regulation of cell cycle cell cycle process developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development multicellular organismal process regulation of developmental process regulation of megakaryocyte differentiation megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity condensed chromosome non-membrane-bounded organelle membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle chromatin silencing complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity condensed chromosome non-membrane-bounded organelle membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex chromatin
D [auth P], E [auth Q]	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding 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 organelle organization 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 organelle organization telomere organization chromosome organization protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	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 CENP-A containing chromatin 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 CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region 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	IPR036060	Zinc finger, C2H2C-type superfamily	Homologous Superfamily
A, B, C	IPR004092	Mbt repeat	Repeat
A, B, C	IPR002515	Zinc finger, C2H2C-type	Repeat
A, B, C	IPR047362	Lethal(3)malignant brain tumor-like protein 1, third MBT repeat	Repeat
A, B, C	IPR047361	Lethal(3)malignant brain tumor-like protein 1, first MBT repeat	Repeat
D [auth P], E [auth Q]	IPR009072	Histone-fold	Homologous Superfamily
D [auth P], E [auth Q]	IPR035425	CENP-T/Histone H4, histone fold	Domain
D [auth P], E [auth Q]	IPR001951	Histone H4	Family
D [auth P], E [auth Q]	IPR019809	Histone H4, conserved site	Conserved Site
D [auth P], E [auth Q]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9Y468	atypical teratoid rhabdoid tumor lung adenocarcinoma malignant glioma osteosarcoma glioblastoma lung cancer medulloblastoma ovarian cancer large cell medulloblastoma malignant ependymoma oligodendroglioma
D [auth P], E [auth Q]	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma allergic rhinitis ulcerative colitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth P], E [auth Q]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.