+Open data
-Basic information
Entry | Database: PDB / ID: 8ebv | ||||||||||||
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Title | Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1 | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information XPC complex / 9+2 motile cilium / core TFIIH complex portion of holo TFIIH complex / MMXD complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly / regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleotide-excision repair, DNA duplex unwinding ...XPC complex / 9+2 motile cilium / core TFIIH complex portion of holo TFIIH complex / MMXD complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly / regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / nuclear pore nuclear basket / CAK-ERCC2 complex / UV protection / embryonic cleavage / G protein-coupled receptor internalization / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cellular response to interleukin-7 / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / 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 / proteasome binding / 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 / 3'-5' DNA helicase activity / RNA Polymerase I Transcription Initiation / centriole replication / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / transcription factor TFIID complex / intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II general transcription initiation factor activity / hematopoietic stem cell differentiation / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / polyubiquitin modification-dependent protein binding / mRNA transport / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / 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 / response to UV / DNA helicase activity / 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 / centriole / hormone-mediated signaling pathway / AURKA Activation by TPX2 / proteasome complex / extracellular matrix organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Josephin domain DUBs / insulin-like growth factor receptor signaling pathway / ciliary basal body / post-embryonic development / regulation of cytokinesis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / chromosome segregation / transcription elongation by RNA polymerase II / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||||||||
Authors | Kim, J. / Yang, W. | ||||||||||||
Funding support | United States, Japan, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ebv.cif.gz | 718.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ebv.ent.gz | 560.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ebv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ebv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ebv_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ebv_validation.xml.gz | 102 KB | Display | |
Data in CIF | 8ebv_validation.cif.gz | 156.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/8ebv ftp://data.pdbj.org/pub/pdb/validation_reports/eb/8ebv | HTTPS FTP |
-Related structure data
Related structure data | 27999MC 8ebsC 8ebtC 8ebuC 8ebwC 8ebxC 8ebyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules ABHIJ
#1: 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 |
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#2: 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 | Mass: 107437.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024R2M8 |
#9: Protein | Mass: 44275.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P54727 |
#10: Protein | 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 |
-General transcription factor IIH subunit ... , 5 types, 5 molecules CDEFG
#3: Protein | 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 |
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#4: Protein | 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 | Mass: 46926.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13888 |
#6: Protein | 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 | 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 |
-DNA chain , 2 types, 2 molecules LM
#11: DNA chain | Mass: 16171.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#12: DNA chain | Mass: 16219.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 8 molecules
#13: Chemical | ChemComp-SF4 / | ||
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#14: Chemical | ChemComp-ZN / #15: Chemical | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: small DNA lesion recognition complex1 / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.58 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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: 3883 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1145832 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65301 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6NMI Accession code: 6NMI / Source name: PDB / Type: experimental model |