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Yorodumi- PDB-2ypw: Atomic model for the N-terminus of TraO fitted in the full-length... -
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-Basic information
Entry | Database: PDB / ID: 2ypw | ||||||
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Title | Atomic model for the N-terminus of TraO fitted in the full-length structure of the bacterial pKM101 type IV secretion system core complex | ||||||
Components | TRAO | ||||||
Keywords | MEMBRANE PROTEIN / BACTERIAL SECRETION / TYPE IV 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: 12.4 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. #1: 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2ypw.cif.gz | 263.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypw.ent.gz | 210.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ypw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ypw_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 2ypw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ypw_validation.xml.gz | 94.9 KB | Display | |
Data in CIF | 2ypw_validation.cif.gz | 120.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypw ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypw | HTTPS FTP |
-Related structure data
Related structure data | 2232MC 2233C 3zbiC 3zbjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-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) / Plasmid: PASK-IBA3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q46704 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRAN, TRAO AND TRAF COMPLEX ENCODED BY PKM101 / Type: COMPLEX |
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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.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 60, TEMPERATURE- 92, INSTRUMENT- NONE, METHOD- BLOT 3 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jan 1, 2008 / 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: 1250 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: 420 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: PHASE FLIPPING, EACH CCD IMAGE | ||||||||||||
Symmetry | Point symmetry: C14 (14 fold cyclic) | ||||||||||||
3D reconstruction | Method: COMMON LINES / Resolution: 12.4 Å / Num. of particles: 3805 / Nominal pixel size: 2.2 Å / Actual pixel size: 2.2 Å Details: THE FILE CORRESPONDS TO AN ATOMIC MODEL FOR THE N -TERMINUS OF TRAO SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2232. (DEPOSITION ID: 11218). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Details: METHOD--RIGID BODY AND FLEXIBLE FITTING | ||||||||||||
Refinement | Highest resolution: 12.4 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 12.4 Å
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