+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27999 | ||||||||||||
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Title | Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1 | ||||||||||||
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 / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / centriole replication / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly ...XPC complex / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / centriole replication / heterotrimeric G-protein binding / Cytosolic iron-sulfur cluster assembly / 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 / DNA 5'-3' helicase / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cellular response to interleukin-7 / DNA 3'-5' helicase / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / proteasome binding / RNA polymerase II general transcription initiation factor activity / 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 / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / intrinsic apoptotic signaling pathway by p53 class mediator / polyubiquitin modification-dependent protein binding / 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 / hormone-mediated signaling pathway / Formation of HIV elongation complex in the absence of HIV Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / 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 / centriole / DNA helicase activity / AURKA Activation by TPX2 / proteasome complex / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / Josephin domain DUBs / isomerase activity / ciliary basal body / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cytokinesis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / chromosome segregation / RNA Polymerase I Promoter Escape / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 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_27999.map.gz | 9.5 MB | EMDB map data format | |
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Header (meta data) | emd-27999-v30.xml emd-27999.xml | 36.9 KB 36.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27999_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_27999.png | 79.6 KB | ||
Filedesc metadata | emd-27999.cif.gz | 10.6 KB | ||
Others | emd_27999_half_map_1.map.gz emd_27999_half_map_2.map.gz | 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27999 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27999 | HTTPS FTP |
-Validation report
Summary document | emd_27999_validation.pdf.gz | 819.1 KB | Display | EMDB validaton report |
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Full document | emd_27999_full_validation.pdf.gz | 818.6 KB | Display | |
Data in XML | emd_27999_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_27999_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27999 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27999 | HTTPS FTP |
-Related structure data
Related structure data | 8ebvMC 8ebsC 8ebtC 8ebuC 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_27999.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_27999_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27999_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : small DNA lesion recognition complex1
+Supramolecule #1: small DNA lesion recognition complex1
+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: DNA repair protein complementing XP-C cells
+Macromolecule #9: UV excision repair protein RAD23 homolog B
+Macromolecule #10: Centrin-2
+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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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: 3883 / 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 / 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 |