9IOL: Complex of DNA, Ku70/80, and laXLF

Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF. Determined by electron microscopy at 3.46 Å resolution. Released 9 Jul 2025.

Method
Electron microscopy
Resolution
3.46 Å
Organism
Homo sapiens
Chains
5
Atoms
9,036
Mol. weight
169.17 kDa
Ligands
IHP, 2OP
Released
9 Jul 2025

Explore 9IOL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IOL contains 55 α-helices and 52 β-strands across 3 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: 31 helices, 24 β-strands

ElementResiduesLengthSheet
β-strand8-1581
α-helix30-4718
β-strand54-5961
β-strand6511
β-strand77-8481
α-helix88-925
α-helix93-975
α-helix107-12216
β-strand129-13571
α-helix147-15610
β-strand159-16571
α-helix199-22123
β-strand224-22631
α-helix227-2337
α-helix237-2404
α-helix244-2463
β-strand247-25372
β-strand257-268122
α-helix274-2763
β-strand277-28043
β-strand289-29794
α-helix300-3023
β-strand30414
α-helix307-3093
β-strand310-31675
β-strand319-32245
α-helix325-3317
β-strand339-34792
α-helix348-3503
α-helix353-3553
β-strand357-366102
α-helix3671
α-helix371-38717
β-strand389-39682
α-helix402-4032
β-strand404-41292
β-strand417-42372
α-helix427-4293
β-strand43016
α-helix435-4373
α-helix445-4473
α-helix448-46013
β-strand46217
β-strand464-46528
α-helix4731
β-strand474-47528
α-helix479-4813
α-helix483-4842
α-helix485-49915
α-helix505-5095
α-helix510-5167
α-helix518-5192
α-helix520-5256
α-helix527-53610
β-strand540-54129
Chain B: 23 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand37-43710
α-helix46-494
α-helix56-583
α-helix59-7719
β-strand82-88710
β-strand94110
β-strand102-109810
α-helix113-1208
α-helix124-13512
α-helix143-15513
β-strand164-170710
α-helix180-19516
β-strand199-204610
β-strand205111
α-helix2061
α-helix233-2353
β-strand236111
α-helix239-25012
α-helix252-2532
β-strand25717
β-strand260-26237
β-strand268-27477
β-strand27716
α-helix282-2854
β-strand286-28945
β-strand29515
β-strand296-30494
β-strand31014
α-helix313-3153
β-strand316-32273
β-strand325-32953
α-helix331-3377
β-strand344-35297
α-helix353-3553
β-strand366-37057
β-strand375-37629
α-helix378-39215
β-strand394-40187
β-strand409-41687
β-strand419-420212
β-strand426-428312
β-strand431-43667
α-helix440-4423
β-strand44312
α-helix444-4485
α-helix456-46813
β-strand47012
α-helix475-4773
α-helix481-49414
α-helix511-5188
α-helix521-5299
Chain M: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix10-123

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
X-ray repair cross-complementing protein 5Aprotein732Homo sapiensP13010 (AlphaFold model)
X-ray repair cross-complementing protein 6Bprotein609Homo sapiensP12956 (AlphaFold model)
DNA (5'-d(p*cp*gp*cp*tp*gp*cp*cp*gp*ap*tp*tp*cp*gp*tp*cp*gp*ap*cp*cp*t)-3')CDNA23Homo sapiens
DNA (5'-d(p*ap*gp*gp*tp*cp*gp*ap*cp*gp*ap*ap*tp*cp*gp*gp*cp*ap*gp*cp*g)-3')DDNA23Homo sapiens
Peptide from Non-homologous end-joining factor 1Mprotein13Homo sapiensQ9H9Q4 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9IOL_1 X-ray repair cross-complementing protein 5 (chains A)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI
Sequence of entity 2 (B), FASTA
>9IOL_2 X-ray repair cross-complementing protein 6 (chains B)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD
Sequence of entity 3 (C), FASTA
>9IOL_3 DNA (5'-D(P*CP*GP*CP*TP*GP*CP*CP*GP*AP*TP*TP*CP*GP*TP*CP*GP*AP*CP*CP*T)-3') (chains C)
CGCTGCCGATTCGTCGACCTCGC
Sequence of entity 4 (D), FASTA
>9IOL_4 DNA (5'-D(P*AP*GP*GP*TP*CP*GP*AP*CP*GP*AP*AP*TP*CP*GP*GP*CP*AP*GP*CP*G)-3') (chains D)
GCGAGGTCGACGAATCGGCAGCG
Sequence of entity 5 (M), FASTA
>9IOL_5 Peptide from Non-homologous end-joining factor 1 (chains M)
SKVKRKKPRGLFS

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P61
2OP(2S)-2-hydroxypropanoic acidC3 H6 O31

Primary citation

Lactylation of XLF promotes non-homologous end-joining repair and chemoresistance in cancer. Jin, M., Huang, B., Yang, X. et al. Mol Cell (2025) 85:2654-2672.e7. DOI 10.1016/j.molcel.2025.06.019 · PubMed

Other PDB entries of the same protein (UniProt P13010 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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