6SXB: XPF-ERCC1 Cryo-EM Structure, DNA-Bound form

XPF-ERCC1 Cryo-EM Structure, DNA-Bound form. Determined by electron microscopy at 7.9 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 7.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,341
Mol. weight: 143.32 kDa
Released: 11 Mar 2020

Explore 6SXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SXB contains 47 α-helices and 23 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 F: 37 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	20-26	7
β-strand	31-34	4	1
α-helix	41-51	11
β-strand	58-61	4	1
α-helix	66-79	14
α-helix	84-85	2
β-strand	86-87	2	1
α-helix	97-100	4
β-strand	105-108	4	1
α-helix	113-119	7
β-strand	130-134	5	1
α-helix	136-138	3
α-helix	145-152	8
β-strand	160-165	6	1
α-helix	168-170	3
α-helix	178-183	6
β-strand	189-190	2	1
α-helix	198-203	6
β-strand	210-216	7	2
α-helix	220-242	23
α-helix	255-258	4
α-helix	263-269	7
α-helix	279-300	22
α-helix	304-308	5
α-helix	311-320	10
α-helix	326-328	3
α-helix	334-341	8
α-helix	379-397	19
β-strand	408-411	4	2
α-helix	414-426	13
α-helix	429-438	10
β-strand	553-556	4	2
α-helix	563-572	10
β-strand	577-579	3	2
α-helix	584-596	13
β-strand	604-610	7	2
α-helix	614-637	24
β-strand	685-686	2	3
α-helix	688-690	3
α-helix	695-699	5
β-strand	716-719	4	3
β-strand	722-727	6	3
α-helix	731-738	8
α-helix	740-748	9
β-strand	754-760	7	3
α-helix	784-794	11
β-strand	800-803	4	3
α-helix	806-815	10
α-helix	820-824	5
α-helix	846-853	8
α-helix	860-867	8
α-helix	874-878	5
α-helix	881-888	8
α-helix	891-901	11

Chain G: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	4
β-strand	121-123	3	4
β-strand	130-131	2	4
β-strand	136-142	7	4
α-helix	143-148	6
α-helix	153-160	8
β-strand	166-172	7	4
α-helix	181-191	11
β-strand	195-199	5	4
α-helix	202-213	12
α-helix	231-238	8
α-helix	247-256	10
α-helix	260-265	6
α-helix	269-271	3
α-helix	279-290	12
α-helix	295-296	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair endonuclease XPF	F	protein	916	Homo sapiens	Q92889 (AlphaFold model)
DNA excision repair protein ERCC-1	G	protein	297	Homo sapiens	P07992 (AlphaFold model)
DNA (5'-d(pcpapgpaptpgpcptpgpa)-3')	C	DNA	10	Homo sapiens
DNA (5'-d(tpcpapgpcpaptpcptpg)-3')	D	DNA	10	Homo sapiens

Sequence of entity 1 (F), FASTA

>6SXB_1 DNA repair endonuclease XPF (chains F)
MESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGADRLLYHFLQLHCHPACLVL
VLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEVYTQGGVIFATSRILVVDFLT
DRIPSDLITGILVYRAHRIIESCQEAFILRLFRQKNKRGFIKAFTDNAVAFDTGFCHVER
VMRNLFVRKLYLWPRFHVAVNSFLEQHKPEVVEIHVSMTPTMLAIQTAILDILNACLKEL
KCHNPSLEVEDLSLENAIGKPFDKTIRHYLDPLWHQLGAKTKSLVQDLKILRTLLQYLSQ
YDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARARVYHLPDAKMSKKEKISEK
MEIKEGEETKKELVLESNPKWEALTEVLKEIEAENKESEALGGPGQVLICASDDRTCSQL
RDYITLGAEAFLLRLYRKTFEKDSKAEEVWMKFRKEDSSKRIRKSHKRPKDPQNKERAST
KERTLKKKKRKLTLTQMVGKPEELEEEGDVEEGYRREISSSPESCPEEIKHEEFDVNLSS
DAAFGILKEPLTIIHPLLGCSDPYALTRVLHEVEPRYVVLYDAELTFVRQLEIYRASRPG
KPLRVYFLIYGGSTEEQRYLTALRKEKEAFEKLIREKASMVVPEEREGRDETNLDLVRGT
ASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTP
EMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEIS
SNDISSKLTLLTLHFPRLRILWCPSPHATAELFEELKQSKPQPDAATALAITADSETLPE
SEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDF
IHTSFAEVVSKGKGKK

Sequence of entity 2 (G), FASTA

>6SXB_2 DNA excision repair protein ERCC-1 (chains G)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

Sequence of entity 3 (C), FASTA

>6SXB_3 DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3') (chains C)
CAGATGCTGA

Sequence of entity 4 (D), FASTA

>6SXB_4 DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3') (chains D)
TCAGCATCTG

Primary citation

Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation. Jones, M., Beuron, F., Borg, A. et al. Nat Commun (2020) 11:1120-1120. DOI 10.1038/s41467-020-14856-2 · 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
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
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
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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