2QM4 | pdb_00002qm4

Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor

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)
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)
C	SCOP2 Family	XLF-Cernunnos	8044652	4004063	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	3001502	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8051827	3001319	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051828	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)
D	XLF_N	e2qm4D1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XLF_N	ECOD (1.6)
D	XLF_like	e2qm4D2	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XLF_like	ECOD (1.6)
D	XLF_C	e2qm4D3	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: XLF_C	ECOD (1.6)
C	XLF_N	e2qm4C1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XLF_N	ECOD (1.6)
C	XLF_like	e2qm4C2	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XLF_like	ECOD (1.6)
C	XLF_C	e2qm4C3	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: XLF_C	ECOD (1.6)
B	XLF_N	e2qm4B1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XLF_N	ECOD (1.6)
B	XLF_like	e2qm4B2	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XLF_like	ECOD (1.6)
B	XLF_C	e2qm4B3	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: XLF_C	ECOD (1.6)
A	XLF_N	e2qm4A1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XLF_N	ECOD (1.6)
A	XLF_like	e2qm4A2	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XLF_like	ECOD (1.6)
A	XLF_C	e2qm4A3	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: XLF_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
A, B, C, D	PF21928	XLF protein coiled-coil region (XLF_CC)	XLF protein coiled-coil region	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Non-homologous end-joining factor 1	DNA binding binding DNA end binding nucleic acid 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR052287	Non-homologous end-joining factor	Family
A, B, C, D	IPR015381	XLF-like, N-terminal	Domain
A, B, C, D	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR053829	XLF-like, coiled-coil region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

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

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.