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- EMDB-71525: NER dual incision complex - DuIM -

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Basic information

Entry
Database: EMDB / ID: EMD-71525
TitleNER dual incision complex - DuIM
Map dataDuIM composite map
Sample
  • Complex: NER dual incision complex
    • Protein or peptide: x 14 types
    • DNA: x 2 types
  • Ligand: x 2 types
KeywordsNER / XPA / XPG / XPF / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / protein localization to chromosome ...positive regulation of t-circle formation / pyrimidine dimer repair by nucleotide-excision repair / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / syncytium formation / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / protein localization to chromosome / DNA replication factor A complex / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / base-excision repair, AP site formation / central nervous system myelin formation / negative regulation of telomere maintenance / single-stranded DNA endodeoxyribonuclease activity / positive regulation of mitotic recombination / resolution of meiotic recombination intermediates / hair cell differentiation / hair follicle maturation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / t-circle formation / mitotic recombination / CAK-ERCC2 complex / bubble DNA binding / embryonic cleavage / post-embryonic hemopoiesis / lateral element / single-stranded telomeric DNA binding / DNA 5'-3' helicase / Removal of the Flap Intermediate / regulation of DNA damage checkpoint / UV protection / isotype switching / regulation of cyclin-dependent protein serine/threonine kinase activity / protein localization to site of double-strand break / G-rich strand telomeric DNA binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / G protein-coupled receptor internalization / chromatin-protein adaptor activity / nuclear thyroid hormone receptor binding / Removal of the Flap Intermediate from the C-strand / response to UV-C / UV-damage excision repair / transcription preinitiation complex / RNA Polymerase I Transcription Termination / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / RNA polymerase II general transcription initiation factor activity / regulation of double-strand break repair via homologous recombination / transcription factor TFIID complex / oogenesis / regulation of mitotic cell cycle phase transition / erythrocyte maturation / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spinal cord development / 3'-5' DNA helicase activity / Impaired BRCA2 binding to RAD51 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / bone mineralization / mRNA Capping / telomeric DNA binding / DNA 3'-5' helicase / 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 / TFIID-class transcription factor complex binding / RNA polymerase II complex binding / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / hemopoiesis / RNA Polymerase I Transcription Initiation / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / embryonic organ development / hematopoietic stem cell differentiation / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / HSF1 activation / protein localization to nucleus / Tat-mediated elongation of the HIV-1 transcript / site of DNA damage
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / XPA protein N-terminal ...XPG/Rad2 endonuclease, eukaryotes / DNA repair protein XPF / : / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / XPA protein N-terminal / Replication factor A protein 3 / Replication factor A protein 3 / 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 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / ERCC4 domain / ERCC4 domain / ERCC4 domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / XPG protein signature 2. / Replication factor A, C-terminal / Replication factor-A C terminal domain / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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 / ATP-dependent helicase Rad3/Chl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / : / 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 / Putative DNA-binding domain superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / OB-fold nucleic acid binding domain / RuvA domain 2-like / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Restriction endonuclease type II-like / PIN-like domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Helix-hairpin-helix domain
Similarity search - Domain/homology
DNA excision repair protein ERCC-1 / Replication protein A 32 kDa subunit / 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 / Replication protein A 70 kDa DNA-binding subunit / DNA excision repair protein ERCC-5 / General transcription factor IIH subunit 1 / Replication protein A 14 kDa subunit / General transcription factor IIH subunit 2 ...DNA excision repair protein ERCC-1 / Replication protein A 32 kDa subunit / 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 / Replication protein A 70 kDa DNA-binding subunit / DNA excision repair protein ERCC-5 / General transcription factor IIH subunit 1 / Replication protein A 14 kDa subunit / 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: 3.4 Å
AuthorsLi CL / Kim J / 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: To Be Published
Title: Nucleotide Excision Repair Uncovered by Pre-incision Complex Structures
Authors: Li CL / Kim J / Yang W
History
DepositionJun 30, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71525.png

Downloads & links

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Map

FileDownload / File: emd_71525.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDuIM composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.009328565 - 0.051526524
Average (Standard dev.)0.00090291904 (±0.0021253391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DuIM DeepEMhancer map

Fileemd_71525_additional_1.map
AnnotationDuIM DeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DuIM half1 map

Fileemd_71525_half_map_1.map
AnnotationDuIM half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DuIM half2 map

Fileemd_71525_half_map_2.map
AnnotationDuIM half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NER dual incision complex

EntireName: NER dual incision complex
Components
  • Complex: NER dual incision complex
    • 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 excision repair protein ERCC-5
    • Protein or peptide: DNA repair endonuclease XPF
    • Protein or peptide: DNA excision repair protein ERCC-1
    • Protein or peptide: DNA repair protein complementing XP-A cells
    • DNA: DNA (Cy5)
    • DNA: DNA
    • Protein or peptide: Replication protein A 70 kDa DNA-binding subunit
    • Protein or peptide: Replication protein A 32 kDa subunit
    • Protein or peptide: Replication protein A 14 kDa subunit
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION

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Supramolecule #1: NER dual incision complex

SupramoleculeName: NER dual incision complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 800 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 excision repair protein ERCC-5

MacromoleculeName: DNA excision repair protein ERCC-5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 133.489562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGVQGLWKLL ECSGRQVSPE ALEGKILAVD ISIWLNQALK GVRDRHGNSI ENPHLLTLFH RLCKLLFFRI RPIFVFDGDA PLLKKQTLV KRRQRKDLAS SDSRKTTEKL LKTFLKRQAI KTAFRSKRDE ALPSLTQVRR ENDLYVLPPL QEEEKHSSEE E DEKEWQER ...String:
MGVQGLWKLL ECSGRQVSPE ALEGKILAVD ISIWLNQALK GVRDRHGNSI ENPHLLTLFH RLCKLLFFRI RPIFVFDGDA PLLKKQTLV KRRQRKDLAS SDSRKTTEKL LKTFLKRQAI KTAFRSKRDE ALPSLTQVRR ENDLYVLPPL QEEEKHSSEE E DEKEWQER MNQKQALQEE FFHNPQAIDI ESEDFSSLPP EVKHEILTDM KEFTKRRRTL FEAMPEESDD FSQYQLKGLL KK NYLNQHI EHVQKEMNQQ HSGHIRRQYE DEGGFLKEVE SRRVVSEDTS HYILIKGIQA KTVAEVDSES LPSSSKMHGM SFD VKSSPC EKLKTEKEPD ATPPSPRTLL AMQAALLGSS SEEELESENR RQARGRNAPA AVDEGSISPR TLSAIKRALD DDED VKVCA GDDVQTGGPG AEEMRINSST ENSDEGLKVR DGKGIPFTAT LASSSVNSAE EHVASTNEGR EPTDSVPKEQ MSLVH VGTE AFPISDESMI KDRKDRLPLE SAVVRHSDAP GLPNGRELTP ASPTCTNSVS KNETHAEVLE QQNELCPYES KFDSSL LSS DDETKCKPNS ASEVIGPVSL QETSSIVSVP SEAVDNVENV VSFNAKEHEN FLETIQEQQT TESAGQDLIS IPKAVEP ME IDSEESESDG SFIEVQSVIS DEELQAEFPE TSKPPSEQGE EELVGTREGE APAESESLLR DNSERDDVDG EPQEAEKD A EDSLHEWQDI NLEELETLES NLLAQQNSLK AQKQQQERIA ATVTGQMFLE SQELLRLFGI PYIQAPMEAE AQCAILDLT DQTSGTITDD SNIWLFGARH VYRNFFNKNK FVEYYQYVDF HNQLGLDRNK LINLAYLLGS DYTEGIPTVG CVTAMEILNE FPGHGLEPL LKFSEWWHEA QKNPKIRPNP HDTKVKKKLR TLQLTPGFPN PAVAEAYLKP VVDDSKGSFL WGKPDLDKIR E FCQRYFGW NRTKTDESLF PVLKQLDAQQ TQLRIDSFFR LAQQEKEDAK RIKSQRLNRA VTCMLRKEKE AAASEIEAVS VA MEKEFEL LDKAKRKTQK RGITNTLEES SSLKRKRLSD SKRKNTCGGF LGETCLSESS DGSSSEDAES SSLMNVQRRT AAK EPKTSA SDSQNSVKEA PVKNGGATTS SSSDSDDDGG KEKMVLVTAR SVFGKKRRKL RRARGRKRKT

UniProtKB: DNA excision repair protein ERCC-5

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Macromolecule #9: DNA repair endonuclease XPF

MacromoleculeName: DNA repair endonuclease XPF / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.694188 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 DIDIEPVTLE 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

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Macromolecule #10: DNA excision repair protein ERCC-1

MacromoleculeName: DNA excision repair protein ERCC-1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.402059 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 VLHEPFLK

UniProtKB: DNA excision repair protein ERCC-1

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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 BL21 (bacteria)
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

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Macromolecule #14: Replication protein A 70 kDa DNA-binding subunit

MacromoleculeName: Replication protein A 70 kDa DNA-binding subunit / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.212977 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MVGQLSEGAI AAIMQKGDTN IKPILQVINI RPITTGNSPP RYRLLMSDGL NTLSSFMLAT QLNPLVEEEQ LSSNCVCQIH RFIVNTLKD GRRVVILMEL EVLKSAEAVG VKIGNPVPYN EGLGQPQVAP PAPAASPAAS SRPQPQNGSS GMGSTVSKAY G ASKTFGKA ...String:
MVGQLSEGAI AAIMQKGDTN IKPILQVINI RPITTGNSPP RYRLLMSDGL NTLSSFMLAT QLNPLVEEEQ LSSNCVCQIH RFIVNTLKD GRRVVILMEL EVLKSAEAVG VKIGNPVPYN EGLGQPQVAP PAPAASPAAS SRPQPQNGSS GMGSTVSKAY G ASKTFGKA AGPSLSHTSG GTQSKVVPIA SLTPYQSKWT ICARVTNKSQ IRTWSNSRGE GKLFSLELVD ESGEIRATAF NE QVDKFFP LIEVNKVYYF SKGTLKIANK QFTAVKNDYE MTFNNETSVM PCEDDHHLPT VQFDFTGIDD LENKSKDSLV DII GICKSY EDATKITVRS NNREVAKRNI YLMDTSGKVV TATLWGEDAD KFDGSRQPVL AIKGARVSDF GGRSLSVLSS STII ANPDI PEAYKLRGWF DAEGQALDGV SISDLKSGGV GGSNTNWKTL YEVKSENLGQ GDKPDYFSSV ATVVYLRKEN CMYQA CPTQ DCNKKVIDQQ NGLYRCEKCD TEFPNFKYRM ILSVNIADFQ ENQWVTCFQE SAEAILGQNA AYLGELKDKN EQAFEE VFQ NANFRSFIFR VRVKVETYND ESRIKATVMD VKPVDYREYG RRLVMSIRRS ALM

UniProtKB: Replication protein A 70 kDa DNA-binding subunit

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Macromolecule #15: Replication protein A 32 kDa subunit

MacromoleculeName: Replication protein A 32 kDa subunit / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.276795 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MWNSGFESYG SSSYGGAGGY TQSPGGFGSP APSQAEKKSR ARAQHIVPCT ISQLLSATLV DEVFRIGNVE ISQVTIVGII RHAEKAPTN IVYKIDDMTA APMDVRQWVD TDDTSSENTV VPPETYVKVA GHLRSFQNKK SLVAFKIMPL EDMNEFTTHI L EVINAHMV ...String:
MWNSGFESYG SSSYGGAGGY TQSPGGFGSP APSQAEKKSR ARAQHIVPCT ISQLLSATLV DEVFRIGNVE ISQVTIVGII RHAEKAPTN IVYKIDDMTA APMDVRQWVD TDDTSSENTV VPPETYVKVA GHLRSFQNKK SLVAFKIMPL EDMNEFTTHI L EVINAHMV LSKANSQPSA GRAPISNPGM SEAGNFGGNS FMPANGLTVA QNQVLNLIKA CPRPEGLNFQ DLKNQLKHMS VS SIKQAVD FLSNEGHIYS TVDDDHFKST DAE

UniProtKB: Replication protein A 32 kDa subunit

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Macromolecule #16: Replication protein A 14 kDa subunit

MacromoleculeName: Replication protein A 14 kDa subunit / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.583714 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MVDMMDLPRS RINAGMLAQF IDKPVCFVGR LEKIHPTGKM FILSDGEGKN GTIELMEPLD EEISGIVEVV GRVTAKATIL CTSYVQFKE DSHPFDLGLY NEAVKIIHDF PQFYPLGIVQ HD

UniProtKB: Replication protein A 14 kDa subunit

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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)

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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)

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMKOAcpotassium acetate
25.0 mMTris2-Amino-2-(hydroxymethyl)propane-1,3-diol
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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6 / Number real images: 52926 / Average exposure time: 3.0 sec. / Average electron dose: 52.5 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

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 140332
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8ebt

source_name: PDB, initial_model_type: experimental modelC7CAD

6sxa

source_name: PDB, initial_model_type: experimental modelXPF/ERCC1

1l1o

source_name: PDB, initial_model_type: experimental modelRPA trimerization core

1jmc

source_name: PDB, initial_model_type: experimental modelRPA70

6tus

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

PDB-9pd4:
NER dual incision complex - DuIM

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