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Open data
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Basic information
| Entry | Database: PDB / ID: 8ebx | ||||||||||||
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| Title | XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) | ||||||||||||
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Keywords | DNA BINDING PROTEIN/DNA / protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||||||||
| Function / homology | Function and homology informationnucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / Cytosolic iron-sulfur cluster assembly / heterotrimeric G-protein binding / transcription export complex 2 ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / Cytosolic iron-sulfur cluster assembly / heterotrimeric G-protein binding / transcription export complex 2 / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / nuclear pore nuclear basket / 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 / sperm principal piece / 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 / centriole replication / 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 / SUMOylation of DNA damage response and repair proteins / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / mRNA export from nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription by RNA polymerase I / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA Polymerase II Pre-transcription Events / Recruitment of mitotic centrosome proteins and complexes / centriole / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / transcription-coupled nucleotide-excision repair / sperm midpiece / AURKA Activation by TPX2 / DNA helicase activity / regulation of cytokinesis / 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 / microtubule cytoskeleton organization / NoRC negatively regulates rRNA expression / transcription by RNA polymerase II / DNA Damage Recognition in GG-NER / intracellular protein localization / spindle / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / G-protein beta/gamma-subunit complex binding / apical part of cell / 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 / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / protein transport / 4 iron, 4 sulfur cluster binding / response to oxidative stress Similarity search - Function | ||||||||||||
| Biological species | Homo sapiens (human)synthetic construct (others) | ||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Kim, J. / Yang, W. | ||||||||||||
| Funding support | United States, Japan, 3items
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Citation | Journal: Nature / Year: 2023Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8ebx.cif.gz | 657.3 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8ebx.ent.gz | 506.7 KB | Display | PDB format |
| PDBx/mmJSON format | 8ebx.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/8ebx ftp://data.pdbj.org/pub/pdb/validation_reports/eb/8ebx | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 28001MC ![]() 8ebsC ![]() 8ebtC ![]() 8ebuC ![]() 8ebvC ![]() 8ebwC ![]() 8ebyC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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Components
-Protein , 5 types, 5 molecules ABHJK
| #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: ![]() |
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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: ![]() |
| #8: Protein | 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: ![]() |
| #9: 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: ![]() |
| #10: Protein | Mass: 31422.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: ![]() |
-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: ![]() |
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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: ![]() |
| #5: Protein | 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: ![]() |
| #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: ![]() |
| #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: ![]() |
-DNA chain , 2 types, 2 molecules LM
| #11: DNA chain | Mass: 12175.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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| #12: DNA chain | Mass: 12183.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 9 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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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: small DNA lesion recognition complex3 / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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| Molecular weight | Value: 0.61 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
| Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
| Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
| 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 |
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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 |
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Processing
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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103713 / 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: 6RO4 Accession code: 6RO4 / Source name: PDB / Type: experimental model |
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About Yorodumi




Homo sapiens (human)
United States,
Japan, 3items
Citation















PDBj


















































FIELD EMISSION GUN
