1IK9 | pdb_00001ik9

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

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)
B	d1ik9b1	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	d1ik9b2	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)
A	d1ik9a1	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	d1ik9a2	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)
C	SCOP2 Family	DNA ligase IV Xrcc4-binding domain-like	8046397	4005059	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	DNA ligase IV Xrcc4-binding domain-like	8095958	3002713	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8036636	3001502	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	SCOP2B (2022-06-29)
A	SCOP2 Family	XRCC4, N-terminal domain	8024254	4002483	SCOP2 (2022-06-29)
A	SCOP2 Family	XRCC4, C-terminal oligomerization domain	8024257	4003793	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	XRCC4 C-terminal oligomerization domain-like	8036636	3001502	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	Autotransporter	e1ik9B1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (develop294)
B	HHH_5	e1ik9B2	A: alpha bundles	X: EGF-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (develop294)
B	RNA_pol_Rpb2_2	e1ik9B3	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: RNA_pol_Rpb2_2	ECOD (develop294)
A	XRCC4	e1ik9A1	A: beta barrels	X: Ribosomal protein L25-like	H: XRCC4, N-terminal domain	T: XRCC4, N-terminal domain	F: XRCC4	ECOD (develop294)
A	XRCC4_CC	e1ik9A4	A: alpha bundles	X: XRCC4 C-terminal oligomerization domain	H: XRCC4 C-terminal oligomerization domain	T: XRCC4 C-terminal oligomerization domain	F: XRCC4_CC	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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
C	DNA LIGASE IV	ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding AMP binding nucleoside phosphate binding ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding AMP binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding purine ribonucleoside triphosphate binding ATP binding DNA binding nucleic acid binding magnesium ion binding metal ion 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 developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development 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 developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development cell division response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cell population proliferation cellular response to ionizing radiation cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation T cell differentiation leukocyte differentiation primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process DNA biosynthetic process stem cell proliferation fibroblast proliferation base-excision repair cellular response to stress DNA damage response response to stress DNA repair somatic stem cell population maintenance maintenance of cell number stem cell population maintenance positive regulation of nervous system development regulation of cellular process regulation of developmental process positive regulation of biological process regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of cellular process regulation of multicellular organismal development regulation of biological process biological regulation positive regulation of cell development positive regulation of multicellular organismal process immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response cell activation involved in immune response somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response production of molecular mediator of immune response immune response B cell activation DNA recombination gene expression immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immunoglobulins somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching V(D)J recombination T cell receptor V(D)J recombination somatic diversification of T cell receptor genes somatic recombination of T cell receptor gene segments pro-B cell differentiation lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining cellular component organization organelle organization chromosome organization cellular component organization or biogenesis positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation establishment of integrated proviral latency viral latency viral process establishment of viral latency neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process single strand break repair DN2 thymocyte differentiation nucleotide-excision repair, DNA gap filling nucleotide-excision repair response to gamma radiation immunoglobulin V(D)J recombination positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization	membrane-bounded organelle protein-containing complex nonhomologous end joining complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle intracellular protein-containing complex DNA ligase IV complex DNA repair complex membrane-bounded organelle protein-containing complex nonhomologous end joining complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle intracellular protein-containing complex DNA ligase IV complex DNA repair complex membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region condensed chromosome membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen DNA-dependent protein kinase-DNA ligase 4 complex
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
C	IPR029710	DNA ligase 4	Family
C	IPR012310	DNA ligase, ATP-dependent, central	Domain
C	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
C	IPR044125	DNA Ligase 4, adenylation domain	Domain
C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C	IPR021536	DNA ligase IV domain	Domain
C	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
C	IPR001357	BRCT domain	Domain
C	IPR036420	BRCT domain superfamily	Homologous Superfamily
C	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
C	IPR000977	DNA ligase, ATP-dependent	Family
C	IPR012309	DNA ligase, ATP-dependent, 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
C	Pharos: P49917	DNA ligase IV deficiency plasma cell myeloma Omenn syndrome Dubowitz syndrome progressive supranuclear palsy Alzheimer disease hematopoietic and lymphoid system neoplasm leukemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell neoplasm severe combined immunodeficiency due to DCLRE1C deficiency atypical teratoid rhabdoid tumor Gaucher disease intellectual disability microcephaly DNA ligase IV deficiency plasma cell myeloma Omenn syndrome Dubowitz syndrome progressive supranuclear palsy Alzheimer disease hematopoietic and lymphoid system neoplasm leukemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell neoplasm severe combined immunodeficiency due to DCLRE1C deficiency atypical teratoid rhabdoid tumor Gaucher disease intellectual disability microcephaly osteosarcoma Pick disease Primary microcephaly glioblastoma large cell medulloblastoma myeloid neoplasm pancreatic intraductal papillary-mucinous neoplasm
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.