9QED: XPF-ERCC1-SLX4(330-555)-SLX4IP complex

Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex. Determined by electron microscopy at 3.2 Å resolution. Released 17 Dec 2025.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Homo sapiens
Chains
4
Atoms
8,748
Mol. weight
214.74 kDa
Released
17 Dec 2025

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

Secondary structure: helices and β-sheets

9QED contains 62 α-helices and 36 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: 41 helices, 19 β-strands

ElementResiduesLengthSheet
α-helix17-2711
β-strand32-3545
α-helix41-5111
β-strand58-6145
α-helix66-7914
β-strand86-8835
α-helix94-10310
β-strand105-10955
α-helix111-12010
β-strand128-13365
α-helix136-1394
α-helix143-15513
β-strand160-16565
α-helix168-1714
α-helix178-1847
β-strand190-19345
α-helix198-2047
β-strand212-21764
α-helix218-2192
α-helix220-24324
α-helix245-2473
α-helix250-2523
α-helix254-2574
α-helix262-2709
α-helix280-30021
α-helix303-31917
α-helix330-34314
α-helix376-3783
α-helix379-39719
β-strand407-41154
α-helix414-42613
α-helix428-43912
α-helix445-45511
β-strand544-54631
β-strand552-55654
α-helix563-5653
α-helix566-5727
β-strand577-58044
α-helix585-59713
β-strand604-61184
α-helix614-64027
β-strand683-68756
α-helix688-6914
α-helix695-7017
β-strand705-70956
β-strand716-71726
β-strand723-72866
α-helix729-73810
α-helix740-75112
β-strand755-76066
α-helix784-79411
β-strand799-80356
α-helix806-81611
α-helix821-8222
α-helix829-8313
α-helix846-8549
α-helix861-8699
α-helix876-8783
α-helix881-8888
α-helix892-90110
Chain B: 12 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand101-10337
α-helix105-1073
α-helix111-1144
β-strand121-12227
β-strand130-13127
β-strand136-14277
α-helix143-1486
α-helix152-1609
β-strand166-17277
α-helix179-19214
β-strand195-19957
α-helix202-21413
α-helix220-2223
α-helix231-24010
α-helix247-25711
α-helix260-2656
α-helix268-2736
α-helix278-28912
Chain C: 5 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand7-1041
β-strand13-1641
β-strand17-2152
α-helix22-232
α-helix30-323
α-helix35-4410
α-helix46-6116
β-strand76-7832
β-strand8313
β-strand85-9172
β-strand97-10044
β-strand105-10734
β-strand108-10921
α-helix1101
β-strand112-11872
β-strand12013
Chain D: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix529-5324
α-helix533-5353
α-helix542-5454
α-helix548-5503

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein SLX4IPCprotein408Homo sapiensQ5VYV7 (AlphaFold model)
DNA repair endonuclease XPFAprotein935Homo sapiensQ92889 (AlphaFold model)
DNA excision repair protein ERCC-1Bprotein297Homo sapiensP07992 (AlphaFold model)
Structure-specific endonuclease subunit SLX4Dprotein271Homo sapiensQ8IY92 (AlphaFold model)
Sequence of entity 1 (C), FASTA
>9QED_1 Protein SLX4IP (chains C)
MASKKFAVKCGNFAVLVDLHILPQGSNKDTSWFSEQKKEEVCLLLKETIDSRVQEYLEVR
KQHRPSNAEFTRSNPLSLKGYGFQITAYFLKRGIRLRCIRSTQNAELCVFPDRFVVCVSQ
LAFSRDLLASQNEDLTERVLHGVSDYFAECAESSLPPSAKLRRNALKEIVKRTETKSSVT
SKSQTRRDTVETSSDSVIAEIARRRNDGQASSSPPSESMGQAKDSIKAAESHWGLPVQKL
EKVNQTQPEDTSGQQKPHPGERLKTGLLSRSPVCSCESASPCPKQSPRVAKTQQKRRNCS
SAEDFDHHGRVSLGSDRLVPREIIVEKSKAVRVLPASELSDPGLLLKQDLAKTTSKEELH
VLESLSSRHLMKNNPGQAQQTGLATNTERLSTIQNSPTKKRKKYERGH
Sequence of entity 2 (A), FASTA
>9QED_2 DNA repair endonuclease XPF (chains A)
MGSSHHHHHHENLYFQSNAMESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGA
DRLLYHFLQLHCHPACLVLVLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEVY
TQGGVIFATSRILVVDFLTDRIPSDLITGILVYRAHRIIESCQEAFILRLFRQKNKRGFI
KAFTDNAVAFDTGFCHVERVMRNLFVRKLYLWPRFHVAVNSFLEQHKPEVVEIHVSMTPT
MLAIQTAILDILNACLKELKCHNPSLEVEDLSLENAIGKPFDKTIRHYLDPLWHQLGAKT
KSLVQDLKILRTLLQYLSQYDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARA
RVYHLPDAKMSKKEKISEKMEIKEGEETKKELVLESNPKWEALTEVLKEIEAENKESEAL
GGPGQVLICASDDRTCSQLRDYITLGAEAFLLRLYRKTFEKDSKAEEVWMKFRKEDSSKR
IRKSHKRPKDPQNKERASTKERTLKKKKRKLTLTQMVGKPEELEEEGDVEEGYRREISSS
PESCPEEIKHEEFDVNLSSDAAFGILKEPLTIIHPLLGCSDPYALTRVLHEVEPRYVVLY
DAELTFVRQLEIYRASRPGKPLRVYFLIYGGSTEEQRYLTALRKEKEAFEKLIREKASMV
VPEEREGRDETNLDLVRGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHR
RGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEF
DPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELFEELKQSKP
QPDAATALAITADSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQ
DELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK
Sequence of entity 3 (B), FASTA
>9QED_3 DNA excision repair protein ERCC-1 (chains B)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP
Sequence of entity 4 (D), FASTA
>9QED_4 Structure-specific endonuclease subunit SLX4 (chains D)
MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAVPQIPECPICGKPFL
TLKSRTSHLKQCAVKMEVGPQLLLQAVRLQTAQPEGSSSPPMFSFSDHSRGLKRRGPTSK
KEPRKRRKVDEAPSEDLLVAMALSRSEMEPGAAVPALRLESAFSERIRPEAENKSRKKKP
PVSPPLLLVQDSETTGRQIEDRVALLLSEEVELSSTPPLPASRILKEGWERAGQCPPPPE
RKQSFLWEGSALTGAWAMEDFYTARLVPPLV

Primary citation

Molecular basis of XPF-ERCC1 targeting to SLX4-dependent DNA repair pathways. Feng, J., Martin, P.R., Kowalski, S. et al. Nat Commun (2025) 17:522-522. DOI 10.1038/s41467-025-67216-3 · PubMed

Other PDB entries of the same protein (UniProt Q5VYV7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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