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- EMDB-28001: XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) -
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Open data
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Basic information
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Title | XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) | ||||||||||||
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![]() | protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | ![]() nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / core TFIIH complex portion of holo TFIIH complex / MMXD complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / core TFIIH complex portion of holo TFIIH complex / MMXD complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / central nervous system myelin formation / response to auditory stimulus / 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 / UV-damage excision repair / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / intercellular bridge / 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 / 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 / protein localization to nucleus / 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 / 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 / extracellular matrix organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / insulin-like growth factor receptor signaling pathway / ciliary basal body / post-embryonic development / regulation of cytokinesis / 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 / NoRC negatively regulates rRNA expression / base-excision repair Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Kim J / Yang W | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 | ![]() | 95.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36.7 KB 36.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 80.7 KB | ||
Filedesc metadata | ![]() | 10.6 KB | ||
Others | ![]() ![]() | 80.9 MB 81 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 715 KB | Display | ![]() |
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Full document | ![]() | 714.5 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ebxMC ![]() 8ebsC ![]() 8ebtC ![]() 8ebuC ![]() 8ebvC ![]() 8ebwC ![]() 8ebyC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28001_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28001_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : small DNA lesion recognition complex3
+Supramolecule #1: small DNA lesion recognition complex3
+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: Centrin-2
+Macromolecule #10: DNA repair protein complementing XP-A cells
+Macromolecule #11: DNA (Ap)
+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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: 3883 / Average exposure time: 2.5 sec. / Average electron dose: 54.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 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 |