9QEE: DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex

Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex. Determined by electron microscopy at 3.4 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 9,789
Mol. weight: 245.86 kDa
Ligands: MN
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9QEE contains 64 α-helices and 44 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, 22 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
α-helix	19-28	10
β-strand	31-35	5	10
α-helix	36	1
α-helix	41-51	11
β-strand	58-61	4	10
α-helix	66-79	14
β-strand	86-88	3	10
α-helix	94-103	10
β-strand	105-109	5	10
α-helix	111-119	9
β-strand	128-133	6	10
α-helix	136-138	3
α-helix	144-155	12
β-strand	160-165	6	10
α-helix	168-171	4
α-helix	178-184	7
β-strand	190-193	4	10
α-helix	198-204	7
α-helix	208-209	2
β-strand	210-216	7	9
α-helix	217-219	3
α-helix	220-243	24
α-helix	250-252	3
α-helix	262-270	9
α-helix	272-275	4
α-helix	280-282	3
α-helix	284-300	17
α-helix	303-319	17
α-helix	330-343	14
β-strand	344-345	2	11
β-strand	372-373	2	11
α-helix	379-397	19
β-strand	406-411	6	9
α-helix	414-426	13
α-helix	428-439	12
β-strand	544-546	3	5
β-strand	552-556	5	9
α-helix	563-565	3
α-helix	566-572	7
β-strand	575-580	6	9
α-helix	585-596	12
β-strand	604-610	7	9
α-helix	614-641	28
β-strand	683-687	5	12
α-helix	688-690	3
α-helix	695-702	8
β-strand	705-709	5	12
β-strand	716-719	4	12
β-strand	722-728	7	12
α-helix	729-738	10
α-helix	740-751	12
β-strand	755-760	6	12
α-helix	784-794	11
β-strand	799-803	5	12
α-helix	806-815	10
α-helix	821-822	2
β-strand	844	1	4
α-helix	846-854	9
α-helix	863-869	7
α-helix	873-878	6
α-helix	881-888	8
α-helix	891-902	12

Chain B: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	1
α-helix	105-107	3
α-helix	113-115	3
β-strand	121-123	3	1
β-strand	130-131	2	1
β-strand	136-137	2	2
β-strand	140-142	3	3
α-helix	143-148	6
α-helix	152-160	9
β-strand	166-167	2	2
β-strand	170-172	3	3
α-helix	179-192	14
β-strand	197-199	3	3
α-helix	202-214	13
α-helix	220-222	3
α-helix	231-238	8
α-helix	247-257	11
α-helix	260-265	6
α-helix	268-273	6
α-helix	279-289	11
β-strand	294	1	4

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	5
β-strand	13-16	4	5
β-strand	17-21	5	6
β-strand	24	1	7
β-strand	27	1	7
α-helix	35-37	3
α-helix	39-44	6
α-helix	46-60	15
β-strand	76-79	4	6
β-strand	83-87	5	6
β-strand	90-91	2	8
β-strand	97-100	4	9
β-strand	105-107	3	9
β-strand	108-109	2	5
β-strand	112-113	2	8
β-strand	114-120	7	6

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	470-473	4
α-helix	476-490	15
α-helix	494-496	3
α-helix	499-506	8
α-helix	507-510	4
α-helix	529-532	4
α-helix	542-545	4
α-helix	548-550	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA excision repair protein ERCC-1	B	protein	297	Homo sapiens	P07992 (AlphaFold model)
Protein SLX4IP	C	protein	408	Homo sapiens	Q5VYV7 (AlphaFold model)
DNA strand 1	U	DNA	50	synthetic construct
DNA strand 2	V	DNA	50	synthetic construct
Structure-specific endonuclease subunit SLX4	D	protein	271	Homo sapiens	Q8IY92 (AlphaFold model)
DNA repair endonuclease XPF	A	protein	935	Homo sapiens	Q92889 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9QEE_1 DNA excision repair protein ERCC-1 (chains B)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

Sequence of entity 2 (C), FASTA

>9QEE_2 Protein SLX4IP (chains C)
MASKKFAVKCGNFAVLVDLHILPQGSNKDTSWFSEQKKEEVCLLLKETIDSRVQEYLEVR
KQHRPSNAEFTRSNPLSLKGYGFQITAYFLKRGIRLRCIRSTQNAELCVFPDRFVVCVSQ
LAFSRDLLASQNEDLTERVLHGVSDYFAECAESSLPPSAKLRRNALKEIVKRTETKSSVT
SKSQTRRDTVETSSDSVIAEIARRRNDGQASSSPPSESMGQAKDSIKAAESHWGLPVQKL
EKVNQTQPEDTSGQQKPHPGERLKTGLLSRSPVCSCESASPCPKQSPRVAKTQQKRRNCS
SAEDFDHHGRVSLGSDRLVPREIIVEKSKAVRVLPASELSDPGLLLKQDLAKTTSKEELH
VLESLSSRHLMKNNPGQAQQTGLATNTERLSTIQNSPTKKRKKYERGH

Sequence of entity 3 (U), FASTA

>9QEE_3 DNA strand 1 (chains U)
TACAGGTGCGACGTAGATGTGGCTATCTCGCTAGATACATAACCGACTAT

Sequence of entity 4 (V), FASTA

>9QEE_4 DNA strand 2 (chains V)
ATAGTCGGTTATGTATCTAGCGAGATAAAGTGTAGATGCAGCGTGGACAT

Sequence of entity 5 (D), FASTA

>9QEE_5 Structure-specific endonuclease subunit SLX4 (chains D)
MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAVPQIPECPICGKPFL
TLKSRTSHLKQCAVKMEVGPQLLLQAVRLQTAQPEGSSSPPMFSFSDHSRGLKRRGPTSK
KEPRKRRKVDEAPSEDLLVAMALSRSEMEPGAAVPALRLESAFSERIRPEAENKSRKKKP
PVSPPLLLVQDSETTGRQIEDRVALLLSEEVELSSTPPLPASRILKEGWERAGQCPPPPE
RKQSFLWEGSALTGAWAMEDFYTARLVPPLV

Sequence of entity 6 (A), FASTA

>9QEE_6 DNA repair endonuclease XPF (chains A)
MGSSHHHHHHENLYFQSNAMESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGA
DRLLYHFLQLHCHPACLVLVLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEVY
TQGGVIFATSRILVVDFLTDRIPSDLITGILVYRAHRIIESCQEAFILRLFRQKNKRGFI
KAFTDNAVAFDTGFCHVERVMRNLFVRKLYLWPRFHVAVNSFLEQHKPEVVEIHVSMTPT
MLAIQTAILDILNACLKELKCHNPSLEVEDLSLENAIGKPFDKTIRHYLDPLWHQLGAKT
KSLVQDLKILRTLLQYLSQYDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARA
RVYHLPDAKMSKKEKISEKMEIKEGEETKKELVLESNPKWEALTEVLKEIEAENKESEAL
GGPGQVLICASDDRTCSQLRDYITLGAEAFLLRLYRKTFEKDSKAEEVWMKFRKEDSSKR
IRKSHKRPKDPQNKERASTKERTLKKKKRKLTLTQMVGKPEELEEEGDVEEGYRREISSS
PESCPEEIKHEEFDVNLSSDAAFGILKEPLTIIHPLLGCSDPYALTRVLHEVEPRYVVLY
DAELTFVRQLEIYRASRPGKPLRVYFLIYGGSTEEQRYLTALRKEKEAFEKLIREKASMV
VPEEREGRDETNLDLVRGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHR
RGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEF
DPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELFEELKQSKP
QPDAATALAITADSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQ
DELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2

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 P07992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A1I 1.9 Å, Crystal Structure of the Central Domain of Human ERCC1
2A1J 2.7 Å, Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1
9QEC 2.9 Å, Cryo-EM structure of the XPF-ERCC1-XPA complex
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
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…
2JNW Solution structure of a ERCC1-XPA heterodimer
2JPD Solution structure of the ERCC1 central domain

Browse structure collections

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