[English] 日本語
Yorodumi- PDB-3zbj: Fitting results in the I-layer of the subnanometer structure of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zbj | ||||||
---|---|---|---|---|---|---|---|
Title | Fitting results in the I-layer of the subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase | ||||||
Components | TRAO PROTEIN | ||||||
Keywords | CELL ADHESION / BACTERIAL SECRETION | ||||||
Function / homology | Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / TraO protein Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å | ||||||
Authors | Rivera-Calzada, A. / Fronzes, R. / Savva, C.G. / Chandran, V. / Lian, P.W. / Laeremans, T. / Pardon, E. / Steyaert, J. / Remaut, H. / Waksman, G. / Orlova, E.V. | ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3zbj.cif.gz | 263.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zbj.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zbj_validation.pdf.gz | 747.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3zbj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3zbj_validation.xml.gz | 95.2 KB | Display | |
Data in CIF | 3zbj_validation.cif.gz | 121 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/3zbj ftp://data.pdbj.org/pub/pdb/validation_reports/zb/3zbj | HTTPS FTP |
-Related structure data
Related structure data | 2233MC 2232C 2ypwC 3zbiC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 12563.215 Da / Num. of mol.: 14 / Fragment: N-TERMINAL DOMAIN, RESIDUES 24-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21 / Plasmid: PASK-IBA3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q46704 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRAN, TRAO AND TRAF COMPLEX ENCODED BY PKM101 DIGESTED WITH 0.02 MG ML- 1 OF ELASTASE FOR 40 MIN AT ROOM TEMPERATURE Type: COMPLEX |
---|---|
Buffer solution | Name: 50 MM TRIS-HCL, 200 MM NACL, 10 MM LDAO / pH: 8 / Details: 50 MM TRIS-HCL, 200 MM NACL, 10 MM LDAO |
Specimen | Conc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 92, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 4 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 12 / Date: Jan 11, 2012 / Details: 4000X4000 CCD |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 66000 X / Calibrated magnification: 68100 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.1 mm |
Specimen holder | Temperature: 95 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GENERIC GATAN |
Image scans | Num. digital images: 262 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: PHASE FLIPPING, EACH CCD IMAGE | ||||||||||||||||||
Symmetry | Point symmetry: C14 (14 fold cyclic) | ||||||||||||||||||
3D reconstruction | Method: COMMON LINES / Resolution: 8.5 Å / Num. of particles: 5430 / Nominal pixel size: 2.2 Å / Actual pixel size: 2.08 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2233. (DEPOSITION ID: 11228). Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY FOLLOWED BY FLEXIBLE FITTING REFINEMENT PROTOCOL--MODELLED | ||||||||||||||||||
Refinement | Highest resolution: 8.5 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.5 Å
|