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Yorodumi- EMDB-2232: Full-length structure of the bacterial pKM101 type IV secretion s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2232 | |||||||||
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Title | Full-length structure of the bacterial pKM101 type IV secretion system core complex | |||||||||
Map data | Reconstruction of the pKM101 type IV secretion system core complex | |||||||||
Sample |
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Keywords | bacterial secretion / type IV secretion / vir / tra | |||||||||
Function / homology | Conjugal transfer, TrbG/VirB9/CagX / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10 / TraB / TrbI / TraO protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.4 Å | |||||||||
Authors | Rivera-Calzada A / Fronzes R / Savva CG / Chandran V / Lian PW / Laeremans T / Pardon E / Steyaert J / Remaut H / Waksman G / Orlova EV | |||||||||
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_2232.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-2232-v30.xml emd-2232.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | EMD-2232_500x500.tif | 314 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2232 | HTTPS FTP |
-Validation report
Summary document | emd_2232_validation.pdf.gz | 222.3 KB | Display | EMDB validaton report |
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Full document | emd_2232_full_validation.pdf.gz | 221.4 KB | Display | |
Data in XML | emd_2232_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2232 | HTTPS FTP |
-Related structure data
Related structure data | 2ypwMC 2233C 3zbiC 3zbjC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2232.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the pKM101 type IV secretion system core complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.22 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
Entire | Name: traN/traO/traF complex encoded by pKM101 |
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Components |
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-Supramolecule #1000: traN/traO/traF complex encoded by pKM101
Supramolecule | Name: traN/traO/traF complex encoded by pKM101 / type: sample / ID: 1000 / Details: monodisperse / 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-virB10 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: BL21 / Location in cell: inner and outer membrane |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c |
Sequence | InterPro: Type IV secretion system, VirB10 / TraB / TrbI |
-Macromolecule #2: traO
Macromolecule | Name: traO / type: protein_or_peptide / ID: 2 / Name.synonym: traO-virB9 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: BL21 / Location in cell: outer membrane |
Molecular weight | Theoretical: 30 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c |
Sequence | InterPro: Conjugal transfer, TrbG/VirB9/CagX |
-Macromolecule #3: traN
Macromolecule | Name: traN / type: protein_or_peptide / ID: 3 / Name.synonym: traN-virB7 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: BL21 / 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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO |
Grid | Details: lacey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 92 K / Instrument: OTHER / Method: blot 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 95 K |
Details | 4000x4000 CCD |
Date | Jan 1, 2008 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 15 µm / Number real images: 420 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 68100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 66000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles picked with BOXER (EMAN) |
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CTF correction | Details: phase flipping, each CCD image |
Final reconstruction | Applied symmetry - Point group: C14 (14 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final map were calculated from 3805 particles / Number images used: 3805 |
Final two d classification | Number classes: 800 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera, Situs |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation |
Output model | PDB-2ypw: |