7M3P | pdb_00007m3p

Xrcc4-Spc110p(164-207) fusion

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d7m3pa1	All beta proteins	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d7m3pa2	Coiled coil proteins	Parallel coiled-coil	XRCC4, C-terminal oligomerization domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d7m3pa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d7m3pb1	All beta proteins	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d7m3pb2	Coiled coil proteins	Parallel coiled-coil	XRCC4, C-terminal oligomerization domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	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	XRCC4_1st	e7m3pA3	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XRCC4_1st	ECOD (1.6)
A	XRCC4_2nd	e7m3pA1	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XRCC4_2nd	ECOD (1.6)
A	XRCC4_3rd_1	e7m3pA2	A: alpha duplicates or obligate multimers	X: XRCC4 C-terminal oligomerization domain (From Topology)	H: XRCC4 C-terminal oligomerization domain (From Topology)	T: XRCC4 C-terminal oligomerization domain	F: XRCC4_3rd_1	ECOD (1.6)
B	XRCC4_1st	e7m3pB2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XRCC4_1st	ECOD (1.6)
B	XRCC4_2nd	e7m3pB3	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XRCC4_2nd	ECOD (1.6)
B	XRCC4_3rd_1	e7m3pB1	A: alpha duplicates or obligate multimers	X: XRCC4 C-terminal oligomerization domain (From Topology)	H: XRCC4 C-terminal oligomerization domain (From Topology)	T: XRCC4 C-terminal oligomerization domain	F: XRCC4_3rd_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06632	XRCC4 N-terminal domain (XRCC4)	XRCC4 N-terminal domain	This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRC ...	This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks [1]. This entry represents the N-terminal beta sandwich domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Xrcc4-Spc110p(164-207)	protein-containing complex binding binding protein binding calmodulin binding structural constituent of cytoskeleton structural molecule activity FHA domain binding protein domain specific binding DNA binding nucleic acid binding enzyme binding identical protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis mitotic spindle elongation spindle elongation microtubule cytoskeleton organization mitotic cell cycle mitotic sister chromatid segregation cell cycle chromosome segregation cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis mitotic spindle elongation spindle elongation microtubule cytoskeleton organization mitotic cell cycle mitotic sister chromatid segregation cell cycle chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation mitotic spindle organization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization gamma-tubulin complex localization localization gamma-tubulin complex localization to mitotic spindle pole body macromolecule localization gamma-tubulin complex localization to nuclear side of mitotic spindle pole body protein-containing complex localization positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly microtubule polymerization or depolymerization positive regulation of protein polymerization positive regulation of cellular process protein polymerization regulation of biological process positive regulation of microtubule nucleation positive regulation of microtubule polymerization or depolymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization biological regulation regulation of microtubule-based process microtubule polymerization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of microtubule nucleation regulation of organelle organization microtubule nucleation regulation of microtubule polymerization regulation of protein polymerization positive regulation of microtubule polymerization regulation of supramolecular fiber organization supramolecular fiber organization regulation of microtubule cytoskeleton organization sexual reproduction reproductive process conjugation with cellular fusion organelle fusion nucleus organization karyogamy karyogamy involved in conjugation with cellular fusion protein localization to microtubule cytoskeleton protein localization to cytoskeleton protein localization to organelle protein localization to spindle pole body protein localization to mitotic spindle pole body protein localization to microtubule organizing center intracellular protein localization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to stimulus response to metal ion response to chemical response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus protein localization to chromosome protein localization to site of double-strand break positive regulation of molecular function regulation of molecular function regulation of catalytic activity positive regulation of catalytic activity positive regulation of ligase activity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair double-strand break repair immune system development multicellular organismal process immunoglobulin production somatic cell DNA recombination multicellular organism development somatic recombination of immunoglobulin gene segments V(D)J recombination anatomical structure development somatic diversification of immune receptors system development developmental process production of molecular mediator of immune response DNA recombination gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process immune system process somatic diversification of immune receptors via germline recombination within a single locus double-strand break repair via nonhomologous end joining	intracellular anatomical structure intracellular membraneless organelle intracellular organelle microtubule organizing center cellular anatomical structure cytoskeleton central plaque of spindle pole body organelle membraneless organelle spindle pole body microtubule cytoskeleton inner plaque of spindle pole body cytoplasm membrane-bounded organelle intracellular anatomical structure intracellular membraneless organelle intracellular organelle microtubule organizing center cellular anatomical structure cytoskeleton central plaque of spindle pole body organelle membraneless organelle spindle pole body microtubule cytoskeleton inner plaque of spindle pole body cytoplasm membrane-bounded organelle nucleus intracellular membrane-bounded organelle cytosol protein-containing complex nonhomologous end joining complex catalytic complex nuclear protein-containing complex intracellular protein-containing complex DNA ligase IV complex DNA repair complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen DNA-dependent protein kinase-DNA ligase 4 complex site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040593	Spindle pole body component 110, C-terminal	Domain
A, B	IPR053963	XRCC4, C-terminal domain	Domain
A, B	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR009089	XRCC4, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
A, B	IPR053961	XRCC4, N-terminal domain	Domain
A, B	IPR010585	DNA repair protein XRCC4	Family
A, B	IPR053962	XRCC4, coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13426	short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer psoriasis tuberculosis intellectual disability malignant ependymoma medulloblastoma osteosarcoma

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.