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- EMDB-4970: Structure of the core TFIIH-XPA-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4970
TitleStructure of the core TFIIH-XPA-DNA complex
Map dataComposite map produced from focused refined maps (deposited as additional EM maps).
Sample
  • Complex: Core TFIIH-XPA-DNA complex
    • Complex: TFIIH-XPA
      • Protein or peptide: x 7 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 2 types
KeywordsComplex / Helicase / Translocase / DNA repair
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / CAK-ERCC2 complex / 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 / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / embryonic organ development / 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 / 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 / DNA topological change / RNA Polymerase I Transcription Initiation / response to UV / 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 / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / transcription-coupled nucleotide-excision repair / DNA helicase activity / TP53 Regulates Transcription of DNA Repair Genes / chromosome segregation / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription elongation by RNA polymerase II / base-excision repair / NoRC negatively regulates rRNA expression / transcription by RNA polymerase II / intracellular protein localization / spindle / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / sequence-specific double-stranded DNA binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 4 iron, 4 sulfur cluster binding / response to oxidative stress / double-stranded DNA binding / 5'-3' DNA helicase activity / damaged DNA binding / nuclear body / protein-macromolecule adaptor activity / nuclear speck / positive regulation of apoptotic process / protein domain specific binding / DNA repair / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
XPA protein N-terminal / 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 / TFIIH subunit Tfb4/GTF2H3 ...XPA protein N-terminal / 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 / 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 / Putative DNA-binding domain superfamily / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / PH-like domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
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 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKokic G / Chernev A / Tegunov D / Dienemann C / Urlaub H / Cramer P
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
German Research FoundationSPP1935 Germany
European Research Council693023
Volkswagen Foundation
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of TFIIH activation for nucleotide excision repair.
Authors: Goran Kokic / Aleksandar Chernev / Dimitry Tegunov / Christian Dienemann / Henning Urlaub / Patrick Cramer /
Abstract: Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large ...Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway.
History
DepositionMay 10, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-6ro4
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ad8
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4970.png

Downloads & links

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Map

FileDownload / File: emd_4970.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map produced from focused refined maps (deposited as additional EM maps).
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04983271 - 0.14952226
Average (Standard dev.)0.00041167595 (±0.0021745525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0500.1500.000

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Supplemental data

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Mask #1

Fileemd_4970_msk_1.map
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Additional map: Half map 1 corresponding to the composite map.

Fileemd_4970_additional_1.map
AnnotationHalf map 1 corresponding to the composite map.
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Additional map: Half map 2 corresponding to the composite map.

Fileemd_4970_additional_2.map
AnnotationHalf map 2 corresponding to the composite map.
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Additional map: Globally refined map.

Fileemd_4970_additional_3.map
AnnotationGlobally refined map.
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Additional map: Half map 1 corresponding to the globally refined map.

Fileemd_4970_additional_4.map
AnnotationHalf map 1 corresponding to the globally refined map.
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Additional map: Half map 2 corresponding to the globally refined map.

Fileemd_4970_additional_5.map
AnnotationHalf map 2 corresponding to the globally refined map.
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Additional map: Focused classified and refined map using a mask...

Fileemd_4970_additional_6.map
AnnotationFocused classified and refined map using a mask around the XPB subunit. This map was one of the maps used to create the composite map.
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Additional map: Focused classified and refined map using a mask...

Fileemd_4970_additional_7.map
AnnotationFocused classified and refined map using a mask around the XPD subunit. This map was one of the maps used to create the composite map.
Projections & Slices
AxesZYX

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Additional map: Focused classified and refined map using a mask...

Fileemd_4970_additional_8.map
AnnotationFocused classified and refined map using a mask around the XPA-TTDA-p52_C-term. region of the complex. This map was one of the maps used to create the composite map.
Projections & Slices
AxesZYX

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Additional map: Focused classified and refined map using a mask...

Fileemd_4970_additional_9.map
AnnotationFocused classified and refined map using a mask around the p52 subunit. This map was one of the maps used to create the composite map.
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Sample components

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Entire : Core TFIIH-XPA-DNA complex

EntireName: Core TFIIH-XPA-DNA complex
Components
  • Complex: Core TFIIH-XPA-DNA complex
    • Complex: TFIIH-XPA
      • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
      • Protein or peptide: General transcription factor IIH subunit 5
      • Protein or peptide: TFIIH basal transcription factor complex helicase XPD subunit
      • Protein or peptide: General transcription factor IIH subunit 3
      • Protein or peptide: General transcription factor IIH subunit 2
      • Protein or peptide: General transcription factor IIH subunit 4
      • Protein or peptide: DNA repair protein complementing XP-A cells
    • Complex: DNA
      • DNA: DNA1
      • DNA: DNA2
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION

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Supramolecule #1: Core TFIIH-XPA-DNA complex

SupramoleculeName: Core TFIIH-XPA-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: TFIIH-XPA

SupramoleculeName: TFIIH-XPA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA1

MacromoleculeName: DNA1 / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.036663 KDa
SequenceString:
(DC)(DA)(DA)(DA)(DG)(DT)(DC)(DA)(DC)(DG) (DA)(DC)(DC)(DT)(DA)(DG)(DA)(DC)(DA)(DC) (DT)(DG)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DG)(DA)(DA)(DT)(DT)(DC)(DA)(DC)(DT)(DG) (DG) (DA)(DG)(DT)(DG)(DA)(DC)(DC)(DT) (DC)

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Macromolecule #2: DNA2

MacromoleculeName: DNA2 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.075698 KDa
SequenceString:
(DG)(DA)(DG)(DG)(DT)(DC)(DA)(DC)(DT)(DC) (DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT)(DT)(DC) (DG)(DA)(DG)(DC)(DT)(DC)(DG)(DC)(DA) (DA)(DC)(DA)(DA)(DT)(DG)(DA)(DG)(DC)(DA) (DC) (DA)(DT)(DA)(DC)(DC)(DT)(DA)(DG) (DT)

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Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPB

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPB
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.404734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #4: General transcription factor IIH subunit 5

MacromoleculeName: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.060362 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K

UniProtKB: General transcription factor IIH subunit 5

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Macromolecule #5: TFIIH basal transcription factor complex helicase XPD subunit

MacromoleculeName: TFIIH basal transcription factor complex helicase XPD subunit
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.021078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 RIEQIAQQL

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

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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: Trichoplusia ni (cabbage looper)
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 2

MacromoleculeName: General transcription factor IIH subunit 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.481996 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #8: General transcription factor IIH subunit 4

MacromoleculeName: General transcription factor IIH subunit 4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #9: DNA repair protein complementing XP-A cells

MacromoleculeName: DNA repair protein complementing XP-A cells / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.422053 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 6 / 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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 4 ul of sample was applied to glow-discharged grids which were blotted for 5s and plunge-frozen in liquid ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio model created in CryoSPARC.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227776
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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