1FU1 | pdb_00001fu1

CRYSTAL STRUCTURE OF HUMAN XRCC4

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)
A	d1fu1a1	All beta proteins	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1fu1a2	Coiled coil proteins	Parallel coiled-coil	XRCC4, C-terminal oligomerization domain	XRCC4, C-terminal oligomerization domain	XRCC4, C-terminal oligomerization domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1fu1b1	All beta proteins	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	XRCC4, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1fu1b2	Coiled coil proteins	Parallel coiled-coil	XRCC4, C-terminal oligomerization domain	XRCC4, C-terminal oligomerization domain	XRCC4, C-terminal oligomerization 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	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)
B	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8036636	3001502	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	BON	e1fu1A1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: BON	ECOD (v294.1)
B	Autotransporter	e1fu1B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (v294.1)
B	HHH_5	e1fu1B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (v294.1)
B		e1fu1B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
A	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
B	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

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
A, B	PF21924	XRCC4 coiled-coil (XRCC4_CC)	XRCC4 coiled-coil	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA REPAIR PROTEIN XRCC4	protein binding binding FHA domain binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity DNA binding nucleic acid binding enzyme binding identical protein binding	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 cellular process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus 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 cellular process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cell cycle cell cycle process positive regulation of molecular function regulation of molecular function regulation of catalytic activity biological regulation 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nonhomologous end joining complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nonhomologous end joining complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle 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 membraneless organelle site of DNA damage intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.