2QM4

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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)
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)
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)

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	1.10.287.450	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF09302	XLF-Cernunnos, XRcc4-like factor, NHEJ component (XLF)	XLF-Cernunnos, XRcc4-like factor, NHEJ component	-	Family

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 organic cyclic compound 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 ligase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity positive regulation of ligase activity cellular response to stimulus DNA ligation involved in DNA repair primary metabolic process DNA metabolic process nucleic acid metabolic process DNA ligation nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair immune system development immunoglobulin production cellular biosynthetic process somatic cell DNA recombination V(D)J recombination somatic recombination of immunoglobulin gene segments organic substance biosynthetic process somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination cellular metabolic process gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process somatic diversification of immune receptors via germline recombination within a single locus T cell activation T cell differentiation double-strand break repair double-strand break repair via nonhomologous end joining	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 cellular anatomical entity intracellular organelle 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 cellular anatomical entity intracellular organelle organelle DNA-dependent protein kinase-DNA ligase 4 complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen fibrillar center intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle 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	IPR015381	XLF, N-terminal	Domain
A, B, C, D	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily

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 National Science Foundation (DBI-1832184), 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 R01GM133198.