+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27996 | ||||||||||||
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Title | Initial DNA-lesion (Cy5) binding by XPC and TFIIH | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 ...XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / heterotrimeric G-protein binding / 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 / CAK-ERCC2 complex / UV protection / nuclear pore nuclear basket / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cellular response to interleukin-7 / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / proteasome binding / mRNA Capping / spinal cord development / 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 / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / centriole replication / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / polyubiquitin modification-dependent protein binding / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA transport / embryonic organ development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / SUMOylation of DNA damage response and repair proteins / Formation of RNA Pol II elongation complex / 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 / hormone-mediated signaling pathway / centriole / post-embryonic development / AURKA Activation by TPX2 / extracellular matrix organization / proteasome complex / G-protein beta/gamma-subunit complex binding / insulin-like growth factor receptor signaling pathway / ciliary basal body / Josephin domain DUBs / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cytokinesis / determination of adult lifespan / ubiquitin binding / isomerase activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / chromosome segregation / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Kim J / Yang W | ||||||||||||
Funding support | United States, Japan, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27996.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-27996-v30.xml emd-27996.xml | 36.8 KB 36.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27996_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_27996.png | 96.6 KB | ||
Filedesc metadata | emd-27996.cif.gz | 10.5 KB | ||
Others | emd_27996_half_map_1.map.gz emd_27996_half_map_2.map.gz | 192.9 MB 192.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27996 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27996 | HTTPS FTP |
-Validation report
Summary document | emd_27996_validation.pdf.gz | 794.3 KB | Display | EMDB validaton report |
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Full document | emd_27996_full_validation.pdf.gz | 793.9 KB | Display | |
Data in XML | emd_27996_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_27996_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27996 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27996 | HTTPS FTP |
-Related structure data
Related structure data | 8ebsMC 8ebtC 8ebuC 8ebvC 8ebwC 8ebxC 8ebyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27996.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27996_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27996_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : bulky DNA lesion recognition complex
+Supramolecule #1: bulky DNA lesion recognition complex
+Macromolecule #1: TFIIH basal transcription factor complex helicase XPB subunit
+Macromolecule #2: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #3: General transcription factor IIH subunit 1
+Macromolecule #4: General transcription factor IIH subunit 4, p52
+Macromolecule #5: General transcription factor IIH subunit 2
+Macromolecule #6: General transcription factor IIH subunit 3
+Macromolecule #7: General transcription factor IIH subunit 5
+Macromolecule #8: Xeroderma pigmentosum, complementation group C, isoform CRA_a
+Macromolecule #9: UV excision repair protein RAD23 homolog B
+Macromolecule #10: Centrin-2
+Macromolecule #11: DNA (Cy5)
+Macromolecule #12: DNA
+Macromolecule #13: IRON/SULFUR CLUSTER
+Macromolecule #14: ZINC ION
+Macromolecule #15: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6243 / Average exposure time: 2.5 sec. / Average electron dose: 54.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |