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Yorodumi- EMDB-2233: Subnanometer structure of the bacterial pKM101 type IV secretion ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2233 | |||||||||
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Title | Subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase | |||||||||
Map data | Subnanometer reconstruction of the pKM101 type IV secretion system core complex digested with elastase | |||||||||
Sample |
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Keywords | bacterial secretion / type IV secretion / vir / tra | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 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: EMBO J / Year: 2013 Title: Structure of a bacterial type IV secretion core complex at subnanometre resolution. Authors: Angel Rivera-Calzada / Rémi Fronzes / Christos G Savva / Vidya Chandran / Pei W Lian / Toon Laeremans / Els Pardon / Jan Steyaert / Han Remaut / Gabriel Waksman / Elena V Orlova / Abstract: Type IV secretion (T4S) systems are able to transport DNAs and/or proteins through the membranes of bacteria. They form large multiprotein complexes consisting of 12 proteins termed VirB1-11 and ...Type IV secretion (T4S) systems are able to transport DNAs and/or proteins through the membranes of bacteria. They form large multiprotein complexes consisting of 12 proteins termed VirB1-11 and VirD4. VirB7, 9 and 10 assemble into a 1.07 MegaDalton membrane-spanning core complex (CC), around which all other components assemble. This complex is made of two parts, the O-layer inserted in the outer membrane and the I-layer inserted in the inner membrane. While the structure of the O-layer has been solved by X-ray crystallography, there is no detailed structural information on the I-layer. Using high-resolution cryo-electron microscopy and molecular modelling combined with biochemical approaches, we determined the I-layer structure and located its various components in the electron density. Our results provide new structural insights on the CC, from which the essential features of T4S system mechanisms can be derived. | |||||||||
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_2233.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-2233-v30.xml emd-2233.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | EMD-2233_500x500.tif | 295.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2233 | HTTPS FTP |
-Validation report
Summary document | emd_2233_validation.pdf.gz | 230.2 KB | Display | EMDB validaton report |
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Full document | emd_2233_full_validation.pdf.gz | 229.3 KB | Display | |
Data in XML | emd_2233_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2233 | HTTPS FTP |
-Related structure data
Related structure data | 3zbiMC 3zbjMC 2232C 2ypwC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2233.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subnanometer reconstruction of the pKM101 type IV secretion system core complex digested with elastase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.08 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 0.02 mg ml...
Entire | Name: traN/traO/traF complex encoded by pKM101 digested with 0.02 mg ml-1 of elastase for 40 min at room temperature |
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Components |
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-Supramolecule #1000: traN/traO/traF complex encoded by pKM101 digested with 0.02 mg ml...
Supramolecule | Name: traN/traO/traF complex encoded by pKM101 digested with 0.02 mg ml-1 of elastase for 40 min at room temperature type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: 14-mer / Number unique components: 3 |
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Molecular weight | Experimental: 880 KDa / Theoretical: 830 KDa / 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 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 | 0.01 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO |
Grid | Details: continuous carbon-coated grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 92 K / Instrument: FEI VITROBOT MARK III / Method: blot 4 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 95 K |
Details | 4000x4000 CCD |
Date | Jan 11, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 15 µm / Number real images: 262 / 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: 1.5 µm / Nominal magnification: 66000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-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: 8.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final map was calculated from 5430 particles / Number images used: 5430 |
Final two d classification | Number classes: 1810 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera, Situs, Sculptor, Flex-EM |
Details | Protocol: Rigid body followed by flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation |
Output model | PDB-3zbi: PDB-3zbj: |