+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6496 | |||||||||
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Title | Electron microscopy of apo yeast Rad4 (XPC homolog) complex | |||||||||
Map data | Reconstruction of apo yeast Rad4 (XPC homolog) complex | |||||||||
Sample |
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Keywords | transcription / DNA repair / stem cells | |||||||||
Function / homology | Function and homology information PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / SUMOylation of DNA damage response and repair proteins / protein deglycosylation / proteasome binding / DNA topological change ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / SUMOylation of DNA damage response and repair proteins / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / : / ubiquitin binding / nucleotide-excision repair / protein-macromolecule adaptor activity / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
Authors | Zhang ET / He Y / Grob P / Fong YW / Nogales E / Tjian R | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Architecture of the human XPC DNA repair and stem cell coactivator complex. Authors: Elisa T Zhang / Yuan He / Patricia Grob / Yick W Fong / Eva Nogales / Robert Tjian / Abstract: The Xeroderma pigmentosum complementation group C (XPC) complex is a versatile factor involved in both nucleotide excision repair and transcriptional coactivation as a critical component of the ...The Xeroderma pigmentosum complementation group C (XPC) complex is a versatile factor involved in both nucleotide excision repair and transcriptional coactivation as a critical component of the NANOG, OCT4, and SOX2 pluripotency gene regulatory network. Here we present the structure of the human holo-XPC complex determined by single-particle electron microscopy to reveal a flexible, ear-shaped structure that undergoes localized loss of order upon DNA binding. We also determined the structure of the complete yeast homolog Rad4 holo-complex to find a similar overall architecture to the human complex, consistent with their shared DNA repair functions. Localized differences between these structures reflect an intriguing phylogenetic divergence in transcriptional capabilities that we present here. Having positioned the constituent subunits by tagging and deletion, we propose a model of key interaction interfaces that reveals the structural basis for this difference in functional conservation. Together, our findings establish a framework for understanding the structure-function relationships of the XPC complex in the interplay between transcription and DNA repair. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6496.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-6496-v30.xml emd-6496.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_6496.tif | 1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6496 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6496.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of apo yeast Rad4 (XPC homolog) complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Apo yeast Rad4 complex
Entire | Name: Apo yeast Rad4 complex |
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Components |
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-Supramolecule #1000: Apo yeast Rad4 complex
Supramolecule | Name: Apo yeast Rad4 complex / type: sample / ID: 1000 Details: Thawed from -80 degrees Celsius and placed on ice immediately prior to grid preparation. Oligomeric state: heterotrimer / Number unique components: 3 |
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Molecular weight | Experimental: 175 KDa / Theoretical: 175 KDa / Method: SDS-PAGE |
-Macromolecule #1: RAD4
Macromolecule | Name: RAD4 / type: protein_or_peptide / ID: 1 / Name.synonym: DNA repair protein RAD4 / Details: contains N-terminal 6xHis and TEV cleavage site / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast / Location in cell: nucleus, cytoplasm |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 |
Sequence | UniProtKB: DNA repair protein RAD4 / GO: nucleotide-excision repair factor 2 complex / InterPro: DNA repair protein Rad4 |
-Macromolecule #2: RAD23
Macromolecule | Name: RAD23 / type: protein_or_peptide / ID: 2 / Name.synonym: UV excision repair protein RAD23 / Details: contains N-terminal 1xFLAG tag / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast / Location in cell: nucleus, cytoplasm |
Molecular weight | Experimental: 55 KDa / Theoretical: 55 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 |
Sequence | UniProtKB: UV excision repair protein RAD23 / GO: nucleotide-excision repair factor 2 complex / InterPro: UV excision repair protein Rad23 |
-Macromolecule #3: RAD33
Macromolecule | Name: RAD33 / type: protein_or_peptide / ID: 3 / Name.synonym: DNA repair protein RAD33 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: yeast / Location in cell: nucleus |
Molecular weight | Experimental: 20 KDa / Theoretical: 20 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 |
Sequence | UniProtKB: DNA repair protein RAD33 / InterPro: Rad33 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.6 Details: 300 mM KCl, 50 mM HEPES, 0.1% NP-40 alternative, 10% glycerol, 0.1 mM EDTA, 1 mM MgCl2, 1 mM TCEP, 1 mM DTT |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein were floated on 2 successive droplets of buffer G (300 mM KCl, 25 mM HEPES ph 7.6, 3% w/v trehalose, 0.01% NP-40 alternative, 1 mM TCEP, 1 mM DTT, 0.1 mM EDTA, 1 ...Details: Grids with adsorbed protein were floated on 2 successive droplets of buffer G (300 mM KCl, 25 mM HEPES ph 7.6, 3% w/v trehalose, 0.01% NP-40 alternative, 1 mM TCEP, 1 mM DTT, 0.1 mM EDTA, 1 mM MgCl2) and subsequently floated on 4 successive 1% w/v uranyl droplets for 10 seconds each. |
Grid | Details: 400 mesh copper grid with thin carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 1.51 µm / Nominal defocus min: 0.49 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: OTHER |
Alignment procedure | Legacy - Astigmatism: Astigmatism was corrected at 80,000 times and 280,000 times magnification. |
Date | Aug 10, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 486 / Average electron dose: 30 e/Å2 / Bits/pixel: 32 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: whole micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 12879 |
Details | Particles were selected by DoGPicker in the Appion pipeline. |