+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5035 | |||||||||
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Title | Structure of a type IV secretion system core complex | |||||||||
Map data | volume | |||||||||
Sample |
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Keywords | bacterial secretion / type IV secretion / vir / tra | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 18.0 Å | |||||||||
Authors | Fronzes R / Schafer E / Wang L / Saibil H / Orlova E / Waksman G | |||||||||
Citation | Journal: Science / Year: 2009 Title: Structure of a type IV secretion system core complex. Authors: Rémi Fronzes / Eva Schäfer / Luchun Wang / Helen R Saibil / Elena V Orlova / Gabriel Waksman / Abstract: Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance ...Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance genes. We report the 15 angstrom resolution cryo-electron microscopy structure of the core complex of a T4SS. The core complex is composed of three proteins, each present in 14 copies and forming a approximately 1.1-megadalton two-chambered, double membrane-spanning channel. The structure is double-walled, with each component apparently spanning a large part of the channel. The complex is open on the cytoplasmic side and constricted on the extracellular side. Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized. | |||||||||
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_5035.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-5035-v30.xml emd-5035.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_5035_1.png | 250.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5035 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5035 | HTTPS FTP |
-Validation report
Summary document | emd_5035_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_5035_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_5035_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5035 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5035 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5035.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | volume | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 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 : traN/traO/traF encoded by pKM101. traN is mutated to replace cys1...
Entire | Name: traN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site) |
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Components |
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-Supramolecule #1000: traN/traO/traF encoded by pKM101. traN is mutated to replace cys1...
Supramolecule | Name: traN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site) type: sample / ID: 1000 / Details: aggregates a high concentration / Oligomeric state: 14 / Number unique components: 3 |
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Molecular weight | Experimental: 1.1 MDa / Theoretical: 1.05 MDa / Method: gel filtration |
-Macromolecule #1: traF
Macromolecule | Name: traF / type: protein_or_peptide / ID: 1 / Name.synonym: traF / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Strain: BL21 / Cell: Escherichia coli / Location in cell: inner membrane |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c |
-Macromolecule #2: traO
Macromolecule | Name: traO / type: protein_or_peptide / ID: 2 / Name.synonym: traO / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Strain: BL21 / Cell: Escherichia coli / Location in cell: outer membrane |
Molecular weight | Theoretical: 30 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c |
-Macromolecule #3: traO
Macromolecule | Name: traO / type: protein_or_peptide / ID: 3 / Name.synonym: traO / Details: non lipidated subunit / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Strain: BL21 / Cell: Escherichia coli / Location in cell: outer membrane |
Molecular weight | Theoretical: 5 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO |
Staining | Type: NEGATIVE / Details: 2% uranyl acetate |
Grid | Details: carbon coated copper grids |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Min: 293 K / Max: 293 K / Average: 293 K |
Date | Jan 1, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 15 / Average electron dose: 20 e/Å2 / Od range: 2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder: side entry room temperature / Specimen holder model: OTHER |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final map was calculated from 300 class averages / Number images used: 1231 |
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Final two d classification | Number classes: 300 |