6SXA: XPF-ERCC1 Cryo-EM Structure, Apo-form

XPF-ERCC1 Cryo-EM Structure, Apo-form. Determined by electron microscopy at 3.6 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,014
Mol. weight: 137.23 kDa
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6SXA contains 52 α-helices and 32 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: 41 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	15-16	2
α-helix	17-28	12
β-strand	32-34	3	1
α-helix	41-52	12
β-strand	58-61	4	1
α-helix	66-79	14
α-helix	84-85	2
β-strand	86-87	2	1
α-helix	94-97	4
α-helix	100-103	4
β-strand	105-108	4	1
α-helix	111-120	10
β-strand	130-133	4	1
α-helix	136-140	5
α-helix	144-152	9
β-strand	160-165	6	1
α-helix	178-184	7
β-strand	191-192	2	1
α-helix	198-201	4
α-helix	203-206	4
α-helix	209	1
β-strand	210	1	2
α-helix	211	1
β-strand	214-216	3	3
α-helix	217-219	3
α-helix	223-242	20
α-helix	255-258	4
α-helix	263-269	7
α-helix	281-300	20
α-helix	303-312	10
α-helix	334-343	10
β-strand	344	1	4
α-helix	345-347	3
β-strand	372	1	4
α-helix	380-396	17
β-strand	407	1	2
β-strand	410-411	2	5
α-helix	414-425	12
α-helix	428-439	12
β-strand	555-556	2	5
α-helix	566-572	7
β-strand	577	1	2
β-strand	580	1	5
α-helix	585-594	10
β-strand	604	1	2
β-strand	608-610	3	3
α-helix	614-637	24
β-strand	683-687	5	6
α-helix	688-691	4
α-helix	695-699	5
β-strand	705-709	5	6
β-strand	716-717	2	6
β-strand	723-728	6	6
α-helix	729-737	9
α-helix	742-751	10
β-strand	755-760	6	6
α-helix	772-777	6
α-helix	784-794	11
β-strand	799-803	5	6
α-helix	806-816	11
α-helix	828-831	4
α-helix	848-854	7
α-helix	860-867	8
α-helix	881-888	8
α-helix	892-901	10

Chain G: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	7
α-helix	113-115	3
β-strand	121-123	3	7
β-strand	130-132	3	7
β-strand	136-138	3	7
β-strand	140-142	3	8
α-helix	143-148	6
α-helix	153-160	8
β-strand	166-167	2	7
β-strand	169-172	4	8
α-helix	181-190	10
β-strand	196-199	4	8
α-helix	204-213	10
α-helix	231-238	8
α-helix	239-241	3
α-helix	247-254	8
α-helix	260-263	4
α-helix	270-272	3
α-helix	279-288	10

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)

Sequence of entity 1 (F), FASTA

>6SXA_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

>6SXA_2 DNA excision repair protein ERCC-1 (chains G)
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTY
AEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVP
WEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQ
ALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLT
TVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

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
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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