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Yorodumi- EMDB-2137: Negative stain EM composite structure (part 2) of the type IV sec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2137 | |||||||||
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Title | Negative stain EM composite structure (part 2) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10 | |||||||||
Map data | Composite map (part 2) of VirB4-VirB7-VirB9-VirB10 | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Williams R / Wallden K / Yan J / Lian PW / Wang L / Thalassinos K / Orlova EV / Waksman G | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system. Authors: Karin Walldén / Robert Williams / Jun Yan / Pei W Lian / Luchun Wang / Konstantinos Thalassinos / Elena V Orlova / Gabriel Waksman / Abstract: Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer ...Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S system is essential for both the assembly of the system and substrate transfer. In this article, we present the crystal structure of the C-terminal domain of Thermoanaerobacter pseudethanolicus VirB4. This structure is strikingly similar to that of another T4S ATPase, VirD4, a protein that shares only 12% sequence identity with VirB4. The VirB4 domain purifies as a monomer, but the full-length protein is observed in a monomer-dimer equilibrium, even in the presence of nucleotides and DNAs. We also report the negative stain electron microscopy structure of the core complex of the T4S system of the Escherichia coli pKM101 plasmid, with VirB4 bound. In this structure, VirB4 is also monomeric and bound through its N-terminal domain to the core's VirB9 protein. Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer. | |||||||||
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_2137.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-2137-v30.xml emd-2137.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | EMD2137.tif | 60.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2137 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2137 | HTTPS FTP |
-Validation report
Summary document | emd_2137_validation.pdf.gz | 181.3 KB | Display | EMDB validaton report |
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Full document | emd_2137_full_validation.pdf.gz | 180.5 KB | Display | |
Data in XML | emd_2137_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2137 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2137 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2137.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map (part 2) of VirB4-VirB7-VirB9-VirB10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.67 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 : TraB/TraN/TraO/TraF complex encoded by pKM101
Entire | Name: TraB/TraN/TraO/TraF complex encoded by pKM101 |
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Components |
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-Supramolecule #1000: TraB/TraN/TraO/TraF complex encoded by pKM101
Supramolecule | Name: TraB/TraN/TraO/TraF complex encoded by pKM101 / type: sample / ID: 1000 Oligomeric state: 14-mer of core complex (TraN/TraO/TraF) and monomer of TraB Number unique components: 4 |
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Molecular weight | Experimental: 1.15 MDa / Theoretical: 1.15 MDa |
-Macromolecule #1: TraB
Macromolecule | Name: TraB / type: protein_or_peptide / ID: 1 / Name.synonym: VirB4 Details: TraB attached to the 1.05 MDa core complex (TraN/TraO/TraF), see EMD-2136 Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: pKM101 plasmid / Location in cell: cell envelope |
Molecular weight | Experimental: 100 KDa / Theoretical: 100 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pCDF Duet1 |
-Macromolecule #2: TraN
Macromolecule | Name: TraN / type: protein_or_peptide / ID: 2 / Name.synonym: VirB7 Details: TraB attached to the 1.05 MDa core complex (TraN/TraO/TraF), see EMD-2136 Number of copies: 14 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: pKM101 plasmid / Location in cell: cell envelope |
Molecular weight | Experimental: 5 KDa / Theoretical: 5 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pCDF Duet1 |
-Macromolecule #3: TraO
Macromolecule | Name: TraO / type: protein_or_peptide / ID: 3 / Name.synonym: VirB9 Details: TraB attached to the 1.05 MDa core complex (TraN/TraO/TraF), see EMD-2136 Number of copies: 14 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: pKM101 plasmid / Location in cell: cell envelope |
Molecular weight | Experimental: 33 KDa / Theoretical: 33 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pCDF Duet1 |
-Macromolecule #4: TraF
Macromolecule | Name: TraF / type: protein_or_peptide / ID: 4 / Name.synonym: VirB10 Details: TraB attached to the 1.05 MDa core complex (TraN/TraO/TraF), see EMD-2136 Number of copies: 14 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: pKM101 plasmid / Location in cell: cell envelope |
Molecular weight | Experimental: 41 KDa / Theoretical: 41 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pCDF Duet1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: NanoW |
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Grid | Details: Glow-discharged continuous carbon |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Dec 22, 2009 |
Image recording | Category: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 12 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: OTHER |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: Phase flipping |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC Details: This map is part of a composite structure of two maps. Number images used: 10000 |
Final two d classification | Number classes: 330 |