2QM4: Non-homologous end-joining factor 1

Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,510
Mol. weight: 108.24 kDa
Released: 11 Dec 2007

Explore 2QM4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QM4 contains 53 α-helices and 31 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	0-9	10
α-helix	12-13	2
β-strand	14-17	4	1
β-strand	22-30	9	1
β-strand	33-39	7	1
β-strand	44-49	6	1
α-helix	51-61	11
α-helix	69-85	17
β-strand	94-100	7	1
β-strand	103-112	10	1
β-strand	115-125	11	1
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-169	33
α-helix	181-184	4
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-228	14

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-10	11
α-helix	12-13	2
β-strand	14-17	4	2
β-strand	22-30	9	2
β-strand	33-39	7	2
β-strand	44-49	6	2
α-helix	51-61	11
α-helix	69-85	17
β-strand	94-100	7	3
β-strand	103-112	10	3
β-strand	115-123	9	3
β-strand	124-125	2	2
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-167	31
α-helix	177-179	3
α-helix	180-184	5
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-225	11

Chain C: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-10	11
α-helix	12-13	2
β-strand	14-17	4	4
β-strand	22-30	9	4
β-strand	33-39	7	4
β-strand	44-50	7	4
α-helix	51-61	11
α-helix	69-85	17
β-strand	94-100	7	5
β-strand	103-111	9	5
β-strand	116-123	8	5
β-strand	124-125	2	4
α-helix	126-127	2
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-169	33
α-helix	177-179	3
α-helix	181-184	4
α-helix	186-192	7
α-helix	193-197	5
α-helix	198-201	4
α-helix	208-225	18

Chain D: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-9	10
α-helix	12-13	2
β-strand	14-17	4	6
β-strand	22-30	9	6
β-strand	33-39	7	6
β-strand	44-50	7	6
α-helix	51-61	11
β-strand	66	1	2
α-helix	69-80	12
β-strand	94-100	7	6
β-strand	103-112	10	6
β-strand	115-125	11	6
α-helix	128-131	4
α-helix	132-136	5
α-helix	137-169	33
α-helix	177-179	3
α-helix	186-196	11
α-helix	198-201	4
α-helix	208-213	6
α-helix	215-227	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-homologous end-joining factor 1	A, B, C, D	protein	235	Homo sapiens	Q9H9Q4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2QM4_1 Non-homologous end-joining factor 1 (chains A, B, C, D)
SGMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRA
KELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFY
WNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDR
LKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQ

Primary citation

Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ. Li, Y., Chirgadze, D.Y., Bolanos-Garcia, V.M. et al. EMBO J (2008) 27:290-300. DOI 10.1038/sj.emboj.7601942 · PubMed

Other PDB entries of the same protein (UniProt Q9H9Q4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2R9A 2.5 Å, Crystal structure of human XLF
7ZYG 2.68 Å, CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
6ERH 2.8 Å, Complex of XLF and heterodimer Ku bound to DNA
9CQ3 2.8 Å, The gap-filling complex with Pol mu engaged in the NHEJ pathway
9N81 2.8 Å, A gap-filling complex with Pol mu engaged in the NHEJ Pathway
6ERG 2.9 Å, Complex of XLF and heterodimer Ku bound to DNA
9CQ6 3.1 Å, The ligation complex in the NHEJ pathway
9N83 3.1 Å, The ligation complex in the NHEJ pathway
9N82 3.3 Å, The ligation (AMP-Lys) complex in the NHEJ pathway
9CQC 3.4 Å, The ligation complex like in the NHEJ pathway
9IOL 3.46 Å, Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF.
3RWR 3.94 Å, Crystal structure of the human XRCC4-XLF complex

Browse structure collections

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