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- 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
TitleAtomic model for the N-terminus of TraO fitted in the full-length structure of the bacterial pKM101 type IV secretion system core complex
ComponentsTRAO
KeywordsMEMBRANE PROTEIN / BACTERIAL SECRETION / TYPE IV SECRETION
Function / homologyConjugal 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 speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.4 Å
AuthorsRivera-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
DepositionNov 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: TRAO
B: TRAO
C: TRAO
D: TRAO
E: TRAO
F: TRAO
G: TRAO
H: TRAO
I: TRAO
J: TRAO
K: TRAO
L: TRAO
M: TRAO
N: TRAO


Theoretical massNumber of molelcules
Total (without water)175,88514
Polymers175,88514
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
TRAO


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRAN, TRAO AND TRAF COMPLEX ENCODED BY PKM101 / Type: COMPLEX
Buffer solutionName: 50 MM TRIS-HCL, 200 MM NACL, 10 MM LDAO / pH: 8 / Details: 50 MM TRIS-HCL, 200 MM NACL, 10 MM LDAO
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 60, TEMPERATURE- 92, INSTRUMENT- NONE, METHOD- BLOT 3 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2008 / Details: 4000X4000 CCD
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 66000 X / Calibrated magnification: 68100 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1250 nm / Cs: 2.1 mm
Specimen holderTemperature: 95 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC GATAN
Image scansNum. digital images: 420
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3IMAGIC3D reconstruction
CTF correctionDetails: PHASE FLIPPING, EACH CCD IMAGE
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: FLEXIBLE FIT / Details: METHOD--RIGID BODY AND FLEXIBLE FITTING
RefinementHighest resolution: 12.4 Å
Refinement stepCycle: LAST / Highest resolution: 12.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12404 0 0 0 12404

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