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- EMDB-71512: NER dual incision complex - NoG -

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Basic information

Entry
Database: EMDB / ID: EMD-71512
TitleNER dual incision complex - NoG
Map dataNER dual incision complex - NoG
Sample
  • Complex: NER dual incision complex without XPG
    • Protein or peptide: x 13 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsNER / XPA / XPG / XPF / DNA binding protein / DNA binding protein-DNA complex
Function / homology
Function and homology information


heteroduplex DNA loop binding / positive regulation of t-circle formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 2 complex / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition ...heteroduplex DNA loop binding / positive regulation of t-circle formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 2 complex / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / negative regulation of telomere maintenance / DNA damage sensor activity / Cytosolic iron-sulfur cluster assembly / single-stranded DNA endonuclease activity / heterotrimeric G-protein binding / resolution of meiotic recombination intermediates / positive regulation of mitotic recombination / hair cell differentiation / response to auditory stimulus / nucleotide-excision repair factor 3 complex / histone H4K20 demethylase activity / nucleotide-excision repair, preincision complex assembly / regulation of proteasomal ubiquitin-dependent protein catabolic process / UV protection / t-circle formation / nuclear pore nuclear basket / CAK-ERCC2 complex / bubble DNA binding / mitotic recombination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / G protein-coupled receptor internalization / DNA 5'-3' helicase / transcription export complex 2 / nuclear thyroid hormone receptor binding / transcription preinitiation complex / sperm principal piece / RNA Polymerase I Transcription Termination / embryonic organ development / negative regulation of telomere maintenance via telomere lengthening / UV-damage excision repair / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HDR through Single Strand Annealing (SSA) / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / ATPase activator activity / proteasome binding / centriole replication / polyubiquitin modification-dependent protein binding / DNA topological change / RNA Polymerase I Transcription Initiation / response to UV / TFIID-class transcription factor complex binding / DNA 3'-5' helicase / protein localization to nucleus / 3'-5' DNA helicase activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / hormone-mediated signaling pathway / SUMOylation of DNA damage response and repair proteins / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / proteasome complex / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / centriole / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / transcription-coupled nucleotide-excision repair / sperm midpiece / telomere maintenance / AURKA Activation by TPX2 / DNA helicase activity / regulation of cytokinesis / site of DNA damage / chromosome segregation
Similarity search - Function
DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / Rad4 beta-hairpin domain 2 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal ...DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / Rad4 beta-hairpin domain 2 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / RAD23A/RAD23B, UBA1 domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / ERCC4 domain / ERCC4 domain / ERCC4 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / : / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ERCC3/RAD25/XPB helicase, C-terminal domain / : / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / UBA/TS-N domain / Putative DNA-binding domain superfamily / RuvA domain 2-like / Restriction endonuclease type II-like / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Ubiquitin associated domain / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / : / DEAH-box subfamily ATP-dependent helicases signature. / SAM-like Helix-hairpin-helix tandem / C1-like domain superfamily
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 1 / Centrin-2 / Lysine-specific demethylase RAD23B / DNA repair protein complementing XP-C cells / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 ...DNA excision repair protein ERCC-1 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 1 / Centrin-2 / Lysine-specific demethylase RAD23B / DNA repair protein complementing XP-C cells / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim J / Li CL / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075037 United States
CitationJournal: Nature / Year: 2026
Title: Pre-incision structures reveal principles of DNA nucleotide excision repair.
Authors: Eric C L Li / Jinseok Kim / Sem J Brussee / Kaoru Sugasawa / Martijn S Luijsterburg / Wei Yang /
Abstract: Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion ...Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion recognition by XPC in global genome repair or by stalled RNA polymerases in transcription-coupled repair, a lesion and surrounding DNA duplex are unwound by TFIIH, which includes the ATPases XPB and XPD, and additional NER factors XPA, XPF, XPG and RPA, to form a DNA bubble comprising around 27 nucleotides. The double strand-single strand (ds-ss) junction-specific endonucleases XPF and XPG cleave DNA on the 5' and 3' sides of the lesion, respectively. Here we report the functional steps and atomic structures of the ATPase-driven and lesion-dependent DNA bubble formation and arrangement of the complete NER factors for dual incision. The unwinding of nearly 30 base pairs of DNA depends mainly on the double strand DNA translocase XPB and the duplex dividers XPA and XPF. XPD binds the lesion strand with XPF at the 5' ds-ss junction. XPF cuts the lesion strand only after XPG binds the 3' ds-ss junction. The ERCC1 subunit of XPF facilitates DNA strand separation and recruitment of RPA to the non-lesion strand. These findings provide insights on the causes of human diseases and potential targets for enhancing chemotherapeutic efficacy.
History
DepositionJun 28, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71512.png

Downloads & links

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Map

FileDownload / File: emd_71512.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNER dual incision complex - NoG
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 220 pix.
= 365.2 Å		1.66 Å/pix.
x 220 pix.
= 365.2 Å		1.66 Å/pix.
x 220 pix.
= 365.2 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.015598386 - 0.123080455
Average (Standard dev.)0.0007470459 (±0.0044844854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71512_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71512_half_map_2.map
AnnotationHalf Map A
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : NER dual incision complex without XPG

EntireName: NER dual incision complex without XPG
Components
  • Complex: NER dual incision complex without XPG
    • Protein or peptide: TFIIH basal transcription factor complex helicase XPB subunit
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
    • Protein or peptide: General transcription factor IIH subunit 1
    • Protein or peptide: General transcription factor IIH subunit 4, p52
    • Protein or peptide: General transcription factor IIH subunit 2
    • Protein or peptide: General transcription factor IIH subunit 3
    • Protein or peptide: General transcription factor IIH subunit 5
    • Protein or peptide: DNA repair protein complementing XP-C cells
    • Protein or peptide: UV excision repair protein RAD23 homolog B
    • Protein or peptide: Centrin-2
    • Protein or peptide: DNA repair protein complementing XP-A cells
    • DNA: DNA (Cy5)
    • DNA: DNA
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: NER dual incision complex without XPG

SupramoleculeName: NER dual incision complex without XPG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 880 KDa

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Macromolecule #1: TFIIH basal transcription factor complex helicase XPB subunit

MacromoleculeName: TFIIH basal transcription factor complex helicase XPB subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.404734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKRDRADRD KKKSRKRHYE DEEDDEEDAP GNDPQEAVPS AAGKQVDESG TKVDEYGAKD YRLQMPLKDD HTSRPLWVAP DGHIFLEAF SPVYKYAQDF LVAIAEPVCR PTHVHEYKLT AYSLYAAVSV GLQTSDITEY LRKLSKTGVP DGIMQFIKLC T VSYGKVKL ...String:
MGKRDRADRD KKKSRKRHYE DEEDDEEDAP GNDPQEAVPS AAGKQVDESG TKVDEYGAKD YRLQMPLKDD HTSRPLWVAP DGHIFLEAF SPVYKYAQDF LVAIAEPVCR PTHVHEYKLT AYSLYAAVSV GLQTSDITEY LRKLSKTGVP DGIMQFIKLC T VSYGKVKL VLKHNRYFVE SCHPDVIQHL LQDPVIRECR LRNSEGEATE LITETFTSKS AISKTAESSG GPSTSRVTDP QG KSDIPMD LFDFYEQMDK DEEEEEETQT VSFEVKQEMI EELQKRCIHL EYPLLAEYDF RNDSVNPDIN IDLKPTAVLR PYQ EKSLRK MFGNGRARSG VIVLPCGAGK SLVGVTAACT VRKRCLVLGN SAVSVEQWKA QFKMWSTIDD SQICRFTSDA KDKP IGCSV AISTYSMLGH TTKRSWEAER VMEWLKTQEW GLMILDEVHT IPAKMFRRVL TIVQAHCKLG LTATLVREDD KIVDL NFLI GPKLYEANWM ELQNNGYIAK VQCAEVWCPM SPEFYREYVA IKTKKRILLY TMNPNKFRAC QFLIKFHERR NDKIIV FAD NVFALKEYAI RLNKPYIYGP TSQGERMQIL QNFKHNPKIN TIFISKVGDT SFDLPEANVL IQISSHGGSR RQEAQRL GR VLRAKKGMVA EEYNAFFYSL VSQDTQEMAY STKRQRFLVD QGYSFKVITK LAGMEEEDLA FSTKEEQQQL LQKVLAAT D LDAEEEVVAG EFGSRSSQAS RRFGTMSSMS GADDTVYMEY HSSRSKAPSK HVHPLFKRFR K

UniProtKB: General transcription and DNA repair factor IIH helicase/translocase subunit XPB

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Macromolecule #2: General transcription and DNA repair factor IIH helicase subunit XPD

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPD
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.018047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV ...String:
MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV PLPAGIYNLD DLKALGRRQG WCPYFLARYS ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN ID NVCIDSM SVNLTRRTLD RCQGNLETLQ KTVLRIKETD EQRLRDEYRR LVEGLREASA ARETDAHLAN PVLPDEVLQE AVP GSIRTA EHFLGFLRRL LEYVKWRLRV QHVVQESPPA FLSGLAQRVC IQRKPLRFCA ERLRSLLHTL EITDLADFSP LTLL ANFAT LVSTYAKGFT IIIEPFDDRT PTIANPILHF SCMDASLAIK PVFERFQSVI ITSGTLSPLD IYPKILDFHP VTMAT FTMT LARVCLCPMI IGRGNDQVAI SSKFETREDI AVIRNYGNLL LEMSAVVPDG IVAFFTSYQY MESTVASWYE QGILEN IQR NKLLFIETQD GAETSVALEK YQEACENGRG AILLSVARGK VSEGIDFVHH YGRAVIMFGV PYVYTQSRIL KARLEYL RD QFQIRENDFL TFDAMRHAAQ CVGRAIRGKT DYGLMVFADK RFARGDKRGK LPRWIQEHLT DANLNLTVDE GVQVAKYF L RQMAQPFHRE DQLGLSLLSL EQLESEETLK RIEQIAQQLD YKDDDDK

UniProtKB: General transcription and DNA repair factor IIH helicase subunit XPD

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Macromolecule #3: General transcription factor IIH subunit 1

MacromoleculeName: General transcription factor IIH subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.116492 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRLNV NATDSSSTSN H KQDVGISA ...String:
MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRLNV NATDSSSTSN H KQDVGISA AFLADVRPQT DGCNGLRYNL TSDIIESIFR TYPAVKMKYA ENVPHNMTEK EFWTRFFQSH YFHRDRLNTG SK DLFAECA KIDEKGLKTM VSLGVKNPLL DLTALEDKPL DEGYGISSVP SASNSKSIKE NSNAAIIKRF NHHSAMVLAA GLR KQEAQN EQTSEPSNMD GNSGDADCFQ PAVKRAKLQE SIEYEDLGKN NSVKTIALNL KKSDRYYHGP TPIQSLQYAT SQDI INSFQ SIRQEMEAYT PKLTQVLSSS AASSTITALS PGGALMQGGT QQAINQMVPN DIQSELKHLY VAVGELLRHF WSCFP VNTP FLEEKVVKMK SNLERFQVTK LCPFQEKIRR QYLSTNLVSH IEEMLQTAYN KLHTWQSRRL MKKT

UniProtKB: General transcription factor IIH subunit 1

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Macromolecule #4: General transcription factor IIH subunit 4, p52

MacromoleculeName: General transcription factor IIH subunit 4, p52 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MESTPSRGLN RVHLQCRNLQ EFLGGLSPGV LDRLYGHPAT CLAVFRELPS LAKNWVMRML FLEQPLPQAA VALWVKKEFS KAQEESTGL LSGLRIWHTQ LLPGGLQGLI LNPIFRQNLR IALLGGGKAW SDDTSQLGPD KHARDVPSLD KYAEERWEVV L HFMVGSPS ...String:
MESTPSRGLN RVHLQCRNLQ EFLGGLSPGV LDRLYGHPAT CLAVFRELPS LAKNWVMRML FLEQPLPQAA VALWVKKEFS KAQEESTGL LSGLRIWHTQ LLPGGLQGLI LNPIFRQNLR IALLGGGKAW SDDTSQLGPD KHARDVPSLD KYAEERWEVV L HFMVGSPS AAVSQDLAQL LSQAGLMKST EPGEPPCITS AGFQFLLLDT PAQLWYFMLQ YLQTAQSRGM DLVEILSFLF QL SFSTLGK DYSVEGMSDS LLNFLQHLRE FGLVFQRKRK SRRYYPTRLA INLSSGVSGA GGTVHQPGFI VVETNYRLYA YTE SELQIA LIALFSEMLY RFPNMVVAQV TRESVQQAIA SGITAQQIIH FLRTRAHPVM LKQTPVLPPT ITDQIRLWEL ERDR LRFTE GVLYNQFLSQ VDFELLLAHA RELGVLVFEN SAKRLMVVTP AGHSDVKRFW KRQKHSS

UniProtKB: General transcription factor IIH subunit 4

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Macromolecule #5: General transcription factor IIH subunit 2

MacromoleculeName: General transcription factor IIH subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.481996 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL ...String:
MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL IIFSSLTTCD PSNIYDLIKT LKAAKIRVSV IGLSAEVRVC TVLARETGGT YHVILDESHY KELLTHHVSP PP ASSSSEC SLIRMGFPQH TIASLSDQDA KPSFSMAHLD GNTEPGLTLG GYFCPQCRAK YCELPVECKI CGLTLVSAPH LAR SYHHLF PLDAFQEIPL EEYNGERFCY GCQGELKDQH VYVCAVCQNV FCVDCDVFVH DSLHCCPGCI HKIPAPSGV

UniProtKB: General transcription factor IIH subunit 2

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Macromolecule #6: General transcription factor IIH subunit 3

MacromoleculeName: General transcription factor IIH subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.416008 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE ...String:
MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE DSALQYMNFM NVIFAAQKQN ILIDACVLDS DSGLLQQACD ITGGLYLKVP QMPSLLQYLL WVFLPDQDQR SQ LILPPPV HVDYRAACFC HRNLIEIGYV CSVCLSIFCN FSPICTTCET AFKISLPPVL KAKKKKLKVS A

UniProtKB: General transcription factor IIH subunit 3

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Macromolecule #7: General transcription factor IIH subunit 5

MacromoleculeName: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.060362 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K

UniProtKB: General transcription factor IIH subunit 5

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Macromolecule #8: DNA repair protein complementing XP-C cells

MacromoleculeName: DNA repair protein complementing XP-C cells / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.171312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVTV KSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE STAFSRSLLP V KPVEIEIE ...String:
MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVTV KSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE STAFSRSLLP V KPVEIEIE TPEQAKTRER SEKIKLEFET YLRRAMKRFN KGVHEDTHKV HLLCLLANGF YRNNICSQPD LHAIGLSIIP AR FTRVLPR DVDTYYLSNL VKWFIGTFTV NAELSASEQD NLQTTLERRF AIYSARDDEE LVHIFLLILR ALQLLTRLVL SLQ PIPLKS ATAKGKKPSK ERLTADPGGS SETSSQVLEN HTKPKTSKGT KQEETFAKGT CRPSAKGKRN KGGRKKRSKP SSSE EDEGP GDKQEKATQR RPHGRERRVA SRVSYKEESG SDEAGSGSDF ELSSGEASDP SDEDSEPGPP KQRKAPAPQR TKAGS KSAS RTHRGSHRKD PSLPVASSSS SSSKRGKKMC SDGEKAEKRS IAGIDQWLEV FCEQEEKWVC VDCVHGVVGQ PLTCYK YAT KPMTYVVGID SDGWVRDVTQ RYDPVWMTVT RKCRVDAEWW AETLRPYQSP FMDREKKEDL EFQAKHMDQP LPTAIGL YK NHPLYALKRH LLKYEAIYPE TAAILGYCRG EAVYSRDCVH TLHSRDTWLK KARVVRLGEV PYKMVKGFSN RARKARLA E PQLREENDLG LFGYWQTEEY QPPVAVDGKV PRNEFGNVYL FLPSMMPIGC VQLNLPNLHR VARKLDIDCV QAITGFDFH GGYSHPVTDG YIVCEEFKDV LLTAWENEQA VIERKEKEKK EKRALGNWKL LAKGLLIRER LKRRYGPKSE AAAPHTDAGG GLSSDEEEG TSSQAEAARI LAASWPQNRE DEEKQKLKGG PKKTKREKKA AASHLFPFEK L

UniProtKB: DNA repair protein complementing XP-C cells

+
Macromolecule #9: UV excision repair protein RAD23 homolog B

MacromoleculeName: UV excision repair protein RAD23 homolog B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.203914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILNDDTALK EYKIDEKNFV VVMVTKPKAV STPAPATTQ QSAPASTTAV TSSTTTTVAQ APTPVPALAP TSTPASITPA SATASSEPAP ASAAKQEKPA EKPAETPVAT S PTATDSTS ...String:
MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILNDDTALK EYKIDEKNFV VVMVTKPKAV STPAPATTQ QSAPASTTAV TSSTTTTVAQ APTPVPALAP TSTPASITPA SATASSEPAP ASAAKQEKPA EKPAETPVAT S PTATDSTS GDSSRSNLFE DATSALVTGQ SYENMVTEIM SMGYEREQVI AALRASFNNP DRAVEYLLMG IPGDRESQAV VD PPQAAST GAPQSSAVAA AAATTTATTT TTSSGGHPLE FLRNQPQFQQ MRQIIQQNPS LLPALLQQIG RENPQLLQQI SQH QEHFIQ MLNEPVQEAG GQGGGGGGGS GGIAEAGSGH MNYIQVTPQE KEAIERLKAL GFPEGLVIQA YFACEKNENL AANF LLQQN FDED

UniProtKB: Lysine-specific demethylase RAD23B

+
Macromolecule #10: Centrin-2

MacromoleculeName: Centrin-2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.769486 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASNFKKANM ASSSQRKRMS PKPELTEEQK QEIREAFDLF DADGTGTIDV KELKVAMRAL GFEPKKEEIK KMISEIDKEG TGKMNFGDF LTVMTQKMSE KDTKEEILKA FKLFDDDETG KISFKNLKRV AKELGENLTD EELQEMIDEA DRDGDGEVSE Q EFLRIMKK TSLY

UniProtKB: Centrin-2

+
Macromolecule #11: DNA repair protein complementing XP-A cells

MacromoleculeName: DNA repair protein complementing XP-A cells / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.422053 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAADGALPE AAALEQPAEL PASVRASIER KRQRALMLRQ ARLAARPYSA TAAAATGGMA NVKAAPKIID TGGGFILEEE EEEEQKIGK VVHQPGPVME FDYVICEECG KEFMDSYLMN HFDLPTCDNC RDADDKHKLI TKTEAKQEYL LKDCDLEKRE P PLKFIVKK ...String:
MAAADGALPE AAALEQPAEL PASVRASIER KRQRALMLRQ ARLAARPYSA TAAAATGGMA NVKAAPKIID TGGGFILEEE EEEEQKIGK VVHQPGPVME FDYVICEECG KEFMDSYLMN HFDLPTCDNC RDADDKHKLI TKTEAKQEYL LKDCDLEKRE P PLKFIVKK NPHHSQWGDM KLYLKLQIVK RSLEVWGSQE ALEEAKEVRQ ENREKMKQKK FDKKVKELRR AVRSSVWKRE TI VHQHEYG PEENLEDDMY RKTCTMCGHE LTYEKM

UniProtKB: DNA repair protein complementing XP-A cells

+
Macromolecule #14: DNA repair endonuclease XPF

MacromoleculeName: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.636156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESGQPARRI AMAPLLEYER QLVLELLDTD GLVVCARGLG ADRLLYHFLQ LHCHPACLVL VLNTQPAEEE YFINQLKIEG VEHLPRRVT NEITSNSRYE VYTQGGVIFA TSRILVVDFL TDRIPSDLIT GILVYRAHRI IESCQEAFIL RLFRQKNKRG F IKAFTDNA ...String:
MESGQPARRI AMAPLLEYER QLVLELLDTD GLVVCARGLG ADRLLYHFLQ LHCHPACLVL VLNTQPAEEE YFINQLKIEG VEHLPRRVT NEITSNSRYE VYTQGGVIFA TSRILVVDFL TDRIPSDLIT GILVYRAHRI IESCQEAFIL RLFRQKNKRG F IKAFTDNA VAFDTGFCHV ERVMRNLFVR KLYLWPRFHV AVNSFLEQHK PEVVEIHVSM TPTMLAIQTA ILDILNACLK EL KCHNPSL EVEDLSLENA IGKPFDKTIR HYLDPLWHQL GAKTKSLVQD LKILRTLLQY LSQYDCVTFL NLLESLRATE KAF GQNSGW LFLDSSTSMF INARARVYHL PDAKMSKKEK ISEKMEIKEG EETKKELVLE SNPKWEALTE VLKEIEAENK ESEA LGGPG QVLICASDDR TCSQLRDYIT LGAEAFLLRL YRKTFEKDSK AEEVWMKFRK EDSSKRIRKS HKRPKDPQNK ERAST KERT LKKKKRKLTL TQMVGKPEEL EEEGDVEEGY RREISSSPES CPEEIKHEEF DVNLSSDAAF GILKEPLTII HPLLGC SDP YALTRVLHEV EPRYVVLYDA ELTFVRQLEI YRASRPGKPL RVYFLIYGGS TEEQRYLTAL RKEKEAFEKL IREKASM VV PEEREGRDET NLDLVRGTAS ADVSTDTRKA GGQEQNGTQQ SIVVDMREFR SELPSLIHRR GIDIEPVTLE VGDYILTP E MCVERKSISD LIGSLNNGRL YSQCISMSRY YKRPVLLIEF DPSKPFSLTS RGALFQEISS NDISSKLTLL TLHFPRLRI LWCPSPHATA ELFEELKQSK PQPDAATALA ITADSETLPE SEKYNPGPQD FLLKMPGVNA KNCRSLMHHV KNIAELAALS QDELTSILG NAANAKQLYD FIHTSFAEVV SKGKGKK

UniProtKB: DNA repair endonuclease XPF

+
Macromolecule #15: DNA excision repair protein ERCC-1

MacromoleculeName: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.598301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY AEYAISQPLE GAGATCPTGS EPLAGETPN QALKPGAKSN SIIVSPRQRG NPVLKFVRNV PWEFGDVIPD YVLGQSTCAL FLSLRYHNLH PDYIHGRLQS L GKNFALRV ...String:
MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVAKPLF RSTQSLPTVD TSAQAAPQTY AEYAISQPLE GAGATCPTGS EPLAGETPN QALKPGAKSN SIIVSPRQRG NPVLKFVRNV PWEFGDVIPD YVLGQSTCAL FLSLRYHNLH PDYIHGRLQS L GKNFALRV LLVQVDVKDP QQALKELAKM CILADCTLIL AWSPEEAGRY LETYKAYEQK PADLLMEKLE QDFVSRVTEC LT TVKSVNK TDSQTLLTTF GSLEQLIAAS REDLALCPGL GPQKARRLFD VLHEPFLKVP

UniProtKB: DNA excision repair protein ERCC-1

+
Macromolecule #12: DNA (Cy5)

MacromoleculeName: DNA (Cy5) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.705611 KDa
SequenceString: (DG)(DC)(DT)(DG)(DC)(DG)(DG)(DT)(DC)(DC) (DG)(DT)(DT)(DG)(DA)(DC)(DG)(DA)(DC)(DA) (DT)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DA) (DA)(DC)(DG)(DA)(DT)(DG)(DC)(DC)(DA)(DC) (DT) (DT)(DC)(DA)(DG)(DC)(DA) ...String:
(DG)(DC)(DT)(DG)(DC)(DG)(DG)(DT)(DC)(DC) (DG)(DT)(DT)(DG)(DA)(DC)(DG)(DA)(DC)(DA) (DT)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DA) (DA)(DC)(DG)(DA)(DT)(DG)(DC)(DC)(DA)(DC) (DT) (DT)(DC)(DA)(DG)(DC)(DA)(DT)(DT) (DG)(DC)(DA)(DC)(DT)(DC)(DA)(DT)(DG)(DT) (DT)(DC) (DT)(DG)(VM6)(DC)(DA)(DC)(DT) (DA)(DG)(DT)(DA)(DC)(DT)(DA)(DC)(DG)(DA) (DC)(DT) (DA)(DC)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DT)(DC)(DG)(DA)

+
Macromolecule #13: DNA

MacromoleculeName: DNA / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 29.180648 KDa
SequenceString: (DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DG)(DT)(DA)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT) (DG)(DT)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DA) (DT) (DG)(DA)(DG)(DT)(DA)(DC) ...String:
(DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DG)(DT)(DA)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT) (DG)(DT)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DA) (DT) (DG)(DA)(DG)(DT)(DA)(DC)(DA)(DA) (DT)(DA)(DC)(DT)(DG)(DA)(DA)(DG)(DT)(DG) (DG)(DC) (DA)(DT)(DC)(DG)(DT)(DT)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DA)(DT)(DG)(DT) (DC)(DG)(DT) (DC)(DA)(DA)(DC)(DG)(DG) (DA)(DC)(DC)(DG)(DC)(DA)(DG)(DC)

+
Macromolecule #16: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 16 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #18: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
25.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
100.0 mMKClPotassium Chloride
2.0 mMCaCl2Calcium Chloride
2.0 mMTCEP(Tris(2-carboxyethyl)phospine)
1.0 %GlycerolGlycerol
0.05 %C14H28O6Octyl Glucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 81380
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8ebs

source_name: PDB, initial_model_type: experimental model

8ebt

source_name: PDB, initial_model_type: experimental model

8ebu

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9pcp:
NER dual incision complex - NoG

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