9QEC: XPF-ERCC1-XPA complex

Cryo-EM structure of the XPF-ERCC1-XPA complex. Determined by electron microscopy at 2.9 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,688
Mol. weight: 170.91 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9QEC contains 53 α-helices and 29 β-strands across 2 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: 42 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	32-35	4	1
α-helix	41-51	11
β-strand	58-61	4	1
α-helix	66-79	14
β-strand	86-88	3	1
α-helix	94-103	10
β-strand	105-109	5	1
α-helix	111-120	10
β-strand	130-134	5	1
α-helix	136-140	5
α-helix	144-155	12
β-strand	160-165	6	1
α-helix	168-170	3
α-helix	178-184	7
β-strand	190-193	4	1
α-helix	198-204	7
α-helix	205-207	3
β-strand	210-216	7	2
α-helix	217-219	3
α-helix	220-243	24
α-helix	245-247	3
α-helix	254-258	5
α-helix	262-270	9
α-helix	271-276	6
α-helix	279-300	22
α-helix	303-319	17
α-helix	330-343	14
β-strand	344-345	2	3
β-strand	372-373	2	3
α-helix	376-378	3
α-helix	379-397	19
α-helix	404-406	3
β-strand	407-411	5	2
α-helix	414-439	26
α-helix	441-442	2
α-helix	444-455	12
β-strand	544-546	3	2
β-strand	552-556	5	2
α-helix	565-573	9
β-strand	577-580	4	2
α-helix	585-596	12
β-strand	604-610	7	2
α-helix	614-640	27
β-strand	683-687	5	4
α-helix	688-691	4
α-helix	695-702	8
β-strand	705-709	5	4
β-strand	716-717	2	4
β-strand	723-728	6	4
α-helix	729-738	10
α-helix	740-751	12
β-strand	755-760	6	4
α-helix	774-776	3
α-helix	784-794	11
β-strand	799-803	5	4
α-helix	806-816	11
α-helix	846-854	9
α-helix	860-869	10
α-helix	873-878	6
α-helix	881-888	8
α-helix	891-901	11
β-strand	904	1	5
α-helix	905-909	5

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	6
α-helix	105-107	3
α-helix	113-115	3
β-strand	121-123	3	6
β-strand	130-131	2	6
β-strand	136-142	7	6
α-helix	143-148	6
α-helix	152-160	9
β-strand	166-172	7	6
α-helix	179-192	14
β-strand	195-199	5	6
α-helix	202-214	13
α-helix	231-240	10
α-helix	247-256	10
β-strand	259	1	5
α-helix	260-265	6
α-helix	268-272	5
α-helix	279-289	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair endonuclease XPF	A	protein	935	Homo sapiens	Q92889 (AlphaFold model)
DNA excision repair protein ERCC-1	B	protein	297	Homo sapiens	P07992 (AlphaFold model)
DNA repair protein complementing XP-A cells	C	protein	273	Homo sapiens	P23025 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9QEC_1 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 2 (B), FASTA

>9QEC_2 DNA excision repair protein ERCC-1 (chains B)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

Sequence of entity 3 (C), FASTA

>9QEC_3 DNA repair protein complementing XP-A cells (chains C)
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMA
NVKAAPKIIDTGGGFILEEEEEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNH
FDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKL
YLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM

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 Q92889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A1J 2.7 Å, Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1
9QED 3.2 Å, Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex
9PD3 3.3 Å, NER dual incision complex - DuIS
9PD4 3.4 Å, NER dual incision complex - DuIM
9QEE 3.4 Å, Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex
6SXA 3.6 Å, XPF-ERCC1 Cryo-EM Structure, Apo-form
9PCP 4.3 Å, NER dual incision complex - NoG
6SXB 7.9 Å, XPF-ERCC1 Cryo-EM Structure, DNA-Bound form
1Z00 Solution structure of the C-terminal domain of ERCC1 complexed with the C-terminal…
2AQ0 Solution structure of the human homodimeric dna repair protein XPF
2KN7 Structure of the XPF-single strand DNA complex
2MUT Solution structure of the F231L mutant ERCC1-XPF dimerization region

Browse structure collections

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