+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5033 | |||||||||
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Title | Structure of a type IV secretion system core complexSecretion | |||||||||
Map data | volume | |||||||||
Sample |
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Keywords | bacterial secretion / type IV secretion / vir / tra | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 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_5033.map.gz | 1.5 MB | EMDB map data format | |
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Header (meta data) | emd-5033-v30.xml emd-5033.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_5033_1.png | 203.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5033 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5033.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | volume | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 complex encoded by pKM101 Digested with 0.002 mg m...
Entire | Name: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius. |
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Components |
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-Supramolecule #1000: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg m...
Supramolecule | Name: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius. type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: 14-mer / Number unique components: 3 |
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Molecular weight | Experimental: 868 KDa / Theoretical: 700 KDa / 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: traN
Macromolecule | Name: traN / type: protein_or_peptide / ID: 3 / Name.synonym: traN / 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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Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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: 22 / Average electron dose: 20 e/Å2 / Od range: 2 / Bits/pixel: 8 |
-Image processing
Final two d classification | Number classes: 150 |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final maps were calculated from 2201 particles / Number images used: 2201 |