3SR2 | pdb_00003sr2

Crystal Structure of Human XLF-XRCC4 Complex

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	SCOP2B (2022-06-29)
F	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)
A	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)
C	Multi_Drug_Res	e3sr2C3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Multi_Drug_Res	ECOD (v294.1)
C	MoCoBD_2	e3sr2C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MoCoBD_2	ECOD (v294.1)
D	HCV_NS2	e3sr2D1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: HCV_NS2	ECOD (v294.1)
D	Multi_Drug_Res	e3sr2D3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Multi_Drug_Res	ECOD (v294.1)
H	HCV_NS2	e3sr2H1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: HCV_NS2	ECOD (v294.1)
H	Multi_Drug_Res	e3sr2H3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Multi_Drug_Res	ECOD (v294.1)
G	HCV_NS2	e3sr2G2	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: HCV_NS2	ECOD (v294.1)
G	Multi_Drug_Res	e3sr2G3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Multi_Drug_Res	ECOD (v294.1)
G	PI3_PI4_kinase	e3sr2G1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3_PI4_kinase	ECOD (v294.1)
E	EF-hand_1, EF-hand_7	e3sr2E1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (v294.1)
F	EF-hand_1, EF-hand_7	e3sr2F1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (v294.1)
B	EF-hand_1, EF-hand_7	e3sr2B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (v294.1)
A	EF-hand_1, EF-hand_7	e3sr2A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
C	1.10.287.450	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
D	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
D	1.10.287.450	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
H	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
H	1.10.287.450	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
G	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
G	1.10.287.450	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
E	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
F	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	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)
A	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D, G, H	PF09302	XLF N-terminal domain (XLF)	XLF N-terminal domain	XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human ...	XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining [1]. This family contains Nej1 (non-homologous end-joining factor) [2], and Lif1, ligase-interacting factor [3]. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining [4]. This entry represents the N-terminal beta sandwich domain of XLF.	Domain
C, D, G, H	PF21928	XLF protein coiled-coil region (XLF_CC)	XLF protein coiled-coil region	-	Coiled-coil
A, B, E, F	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
C, D, G, H	Non-homologous end-joining factor 1	DNA binding binding nucleic acid binding DNA end binding protein binding DNA polymerase binding enzyme binding	response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation multicellular organism development central nervous system development nervous system development system development 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 immune system development immunoglobulin production somatic cell DNA recombination nucleobase-containing compound metabolic process somatic recombination of immunoglobulin gene segments V(D)J recombination somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination primary metabolic process DNA metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process somatic diversification of immune receptors via germline recombination within a single locus metabolic process macromolecule metabolic process T cell activation T cell differentiation cellular response to stimulus double-strand break repair double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis	protein-containing complex nonhomologous end joining complex catalytic complex intracellular protein-containing complex DNA repair complex membrane-bounded organelle intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle DNA-dependent protein kinase-DNA ligase 4 complex protein-containing complex nonhomologous end joining complex catalytic complex intracellular protein-containing complex DNA repair complex membrane-bounded organelle intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle DNA-dependent protein kinase-DNA ligase 4 complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center membraneless organelle nuclear lumen DNA ligase IV complex site of double-strand break site of DNA damage chromosome nucleoplasm
A, B, E, F	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, D, G, H	IPR052287	Non-homologous end-joining factor	Family
C, D, G, H	IPR015381	XLF-like, N-terminal	Domain
C, D, G, H	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
C, D, G, H	IPR053829	XLF-like, coiled-coil region	Domain
A, B, E, F	IPR053963	XRCC4, C-terminal domain	Domain
A, B, E, F	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
A, B, E, F	IPR009089	XRCC4, N-terminal domain superfamily	Homologous Superfamily
A, B, E, F	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
A, B, E, F	IPR053961	XRCC4, N-terminal domain	Domain
A, B, E, F	IPR010585	DNA repair protein XRCC4	Family
A, B, E, F	IPR053962	XRCC4, coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D, G, H	Pharos: Q9H9Q4	Cernunnos-XLF deficiency microcephaly DNA ligase IV deficiency Primary microcephaly intellectual disability
A, B, E, F	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.