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- PDB-8ebs: Initial DNA-lesion (Cy5) binding by XPC and TFIIH -

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Entry
Database: PDB / ID: 8ebs
TitleInitial DNA-lesion (Cy5) binding by XPC and TFIIH
Components
  • (General transcription factor IIH subunit ...) x 5
  • Centrin-2
  • DNA (Cy5)
  • DNA
  • General transcription and DNA repair factor IIH helicase subunit XPD
  • TFIIH basal transcription factor complex helicase XPB subunit
  • UV excision repair protein RAD23 homolog B
  • Xeroderma pigmentosum, complementation group C, isoform CRA_a
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


XPC complex / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly ...XPC complex / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / nuclear pore nuclear basket / UV protection / CAK-ERCC2 complex / embryonic cleavage / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cellular response to interleukin-7 / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / 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 / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / proteasome binding / mRNA Capping / bone mineralization / 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 / erythrocyte maturation / regulation of cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / RNA Polymerase I Transcription Initiation / centriole replication / transcription elongation by RNA polymerase I / DNA topological change / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / mRNA transport / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to UV / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / RNA Polymerase II Pre-transcription Events / Anchoring of the basal body to the plasma membrane / DNA helicase activity / centriole / hormone-mediated signaling pathway / extracellular matrix organization / proteasome complex / AURKA Activation by TPX2 / Josephin domain DUBs / post-embryonic development / insulin-like growth factor receptor signaling pathway / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of cytokinesis / ubiquitin binding / chromosome segregation / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / determination of adult lifespan / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / DNA Damage Recognition in GG-NER
Similarity search - Function
Rad4 beta-hairpin domain 2 / 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 2 / 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 / 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 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / UBA/TS-N domain / Ubiquitin associated domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / UBA-like superfamily / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / EF-hand domain pair / Papain-like cysteine peptidase superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / EF-hand domain pair / helicase superfamily c-terminal domain / Ubiquitin domain profile. / 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 / PH-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Xeroderma pigmentosum, complementation group C, isoform CRA_a / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / Centrin-2 / UV excision repair protein RAD23 homolog B / General transcription factor IIH subunit 2 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Xeroderma pigmentosum, complementation group C, isoform CRA_a / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / Centrin-2 / UV excision repair protein RAD23 homolog B / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsKim, J. / Yang, W.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075037 United States
Japan Society for the Promotion of Science (JSPS)JP16H06307 Japan
Japan Society for the Promotion of Science (JSPS)JP21H03598 Japan
CitationJournal: Nature / Year: 2023
Title: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Authors: Jinseok Kim / Chia-Lung Li / Xuemin Chen / Yanxiang Cui / Filip M Golebiowski / Huaibin Wang / Fumio Hanaoka / Kaoru Sugasawa / Wei Yang /
Abstract: Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA ...Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TFIIH basal transcription factor complex helicase XPB subunit
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: General transcription factor IIH subunit 1
D: General transcription factor IIH subunit 4, p52
E: General transcription factor IIH subunit 2
F: General transcription factor IIH subunit 3
G: General transcription factor IIH subunit 5
H: Xeroderma pigmentosum, complementation group C, isoform CRA_a
I: UV excision repair protein RAD23 homolog B
J: Centrin-2
L: DNA (Cy5)
M: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)585,99420
Polymers585,23512
Non-polymers7598
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules ABHIJ

#1: Protein TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 89404.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19447, DNA helicase
#2: Protein General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 88018.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18074, DNA helicase
#8: Protein Xeroderma pigmentosum, complementation group C, isoform CRA_a /


Mass: 107437.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPC, hCG_27237 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024R2M8
#9: Protein UV excision repair protein RAD23 homolog B / HR23B / hHR23B / XP-C repair-complementing complex 58 kDa protein / p58


Mass: 44275.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23B / Production host: Escherichia coli (E. coli) / References: UniProt: P54727
#10: Protein Centrin-2 / / Caltractin isoform 1


Mass: 19769.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41208

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General transcription factor IIH subunit ... , 5 types, 5 molecules CDEFG

#3: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 62116.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32780
#4: Protein General transcription factor IIH subunit 4, p52 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 46926.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13888
#6: Protein General transcription factor IIH subunit 3 / p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13889
#7: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZYL4

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DNA chain , 2 types, 2 molecules LM

#11: DNA chain DNA (Cy5)


Mass: 16345.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain DNA /


Mass: 16219.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#13: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: bulky DNA lesion recognition complex / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.58 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acid1
2100 mMpotassium chlorideKCl1
30.5 %Glycerol1
42 mMMagnesium chlorideMgCl21
52 mM(Tris(2-carboxyethyl)phosphine)1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 1600 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 54.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6243

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1645921
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278447 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6NMI

6nmi


Accession code: 6NMI / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00231894
ELECTRON MICROSCOPYf_angle_d0.41743579
ELECTRON MICROSCOPYf_dihedral_angle_d15.9412149
ELECTRON MICROSCOPYf_chiral_restr0.0364854
ELECTRON MICROSCOPYf_plane_restr0.0035228

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