2IG0 | pdb_00002ig0

Structure of 53BP1/methylated histone peptide complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2ig0a2	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ig0a1	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, N-terminal domain	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	Tudor/PWWP/MBT domain-like	8041640	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8041642	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	53-BP1_Tudor_C	e2ig0A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_C	ECOD (1.6)
A	53-BP1_Tudor_N	e2ig0A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_N	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)
A	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Dimethylated Histone H4-K20 peptide	DNA binding 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 cellular component organization protein-DNA complex 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 cellular component organization protein-DNA complex 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 localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development 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 negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A	Tumor suppressor p53-binding protein 1	p53 binding protein binding binding histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone binding transcription regulator activity transcription coregulator activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity p53 binding protein binding binding histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone binding transcription regulator activity transcription coregulator activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity ubiquitin-like protein reader activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding transcription coactivator activity sequence-specific DNA binding DNA binding nucleic acid binding telomeric DNA binding damaged DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination regulation of response to stimulus metabolic process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response immune response immune effector process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination positive regulation of lymphocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response positive regulation of isotype switching regulation of B cell activation leukocyte activation involved in immune response positive regulation of immune effector process positive regulation of cellular process positive regulation of immunoglobulin production production of molecular mediator of immune response regulation of isotype switching cell activation macromolecule biosynthetic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation multicellular organismal process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity cell activation involved in immune response positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process positive regulation of leukocyte activation anatomical structure development leukocyte mediated immunity somatic diversification of immune receptors positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response developmental process regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity positive regulation of multicellular organismal process regulation of immune response regulation of production of molecular mediator of immune response isotype switching immune system development positive regulation of lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of biological process lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation gene expression positive regulation of B cell activation adaptive immune response immunoglobulin mediated immune response regulation of immunoglobulin production regulation of lymphocyte mediated immunity double-strand break repair via classical nonhomologous end joining double-strand break repair via nonhomologous end joining localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction signal transduction by p53 class mediator cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling response to X-ray cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus cellular response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle chromosome chromosomal region kinetochore membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome replication fork site of double-strand break site of DNA damage nuclear body chromosome, telomeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR035425	CENP-T/Histone H4, histone fold	Domain
B	IPR001951	Histone H4	Family
B	IPR019809	Histone H4, conserved site	Conserved Site
B	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A	IPR047252	TP53-binding protein 1-like	Family
A	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A	IPR015125	Tumour suppressor p53-binding protein-1, Tudor domain	Domain
A	IPR001357	BRCT domain	Domain
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
A	IPR047249	TP53-binding protein 1-like, first BRCT domain	Domain
A	IPR047250	TP53-binding protein 1-like, second BRCT domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	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
A	Pharos: Q12888	astrocytic tumor lung carcinoma oligodendroglioma Pick disease cancer malignant ependymoma osteosarcoma lung cancer medulloblastoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	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 R01GM157729.