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Yorodumi- EMDB-27997: XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27997 | ||||||||||||
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Title | XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / positive regulation of DNA helicase activity ...nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / transcription export complex 2 / central nervous system myelin formation / response to auditory stimulus / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / 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 / UV-damage excision repair / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / intercellular bridge / 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 / 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 / protein localization to nucleus / 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 / AURKA Activation by TPX2 / post-embryonic development / insulin-like growth factor receptor signaling pathway / ciliary basal body / regulation of cytokinesis / chromosome segregation / 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 / base-excision repair / G-protein beta/gamma-subunit complex binding / multicellular organism growth / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / spindle Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_27997.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-27997-v30.xml emd-27997.xml | 34.5 KB 34.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27997_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_27997.png | 93.7 KB | ||
Others | emd_27997_half_map_1.map.gz emd_27997_half_map_2.map.gz | 152.1 MB 152.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27997 | HTTPS FTP |
-Related structure data
Related structure data | 8ebtMC 8ebsC 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_27997.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_27997_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27997_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : protein DNA complex
+Supramolecule #1: protein DNA complex
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPB
+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
+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: DNA repair protein complementing XP-C cells
+Macromolecule #9: Centrin-2
+Macromolecule #10: DNA repair protein complementing XP-A cells
+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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficient |
Output model | PDB-8ebt: |