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- PDB-3zbj: Fitting results in the I-layer of the subnanometer structure of t... -

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Entry
Database: PDB / ID: 3zbj
TitleFitting results in the I-layer of the subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
ComponentsTRAO PROTEIN
KeywordsCELL ADHESION / BACTERIAL 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: 8.5 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.
CitationJournal: 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
DepositionNov 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2233
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Structure viewerMolecule:
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Assembly

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


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 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: BL21List of strains of Escherichia 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 DIGESTED WITH 0.02 MG ML- 1 OF ELASTASE FOR 40 MIN AT ROOM TEMPERATURE
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.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: 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,

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Jan 11, 2012 / 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: 1500 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: 262
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Flex-EMmodel fitting
2Sculptormodel fitting
3Situsmodel fitting
4UCSF Chimeramodel fitting
5IMAGIC3D reconstruction
CTF correctionDetails: PHASE FLIPPING, EACH CCD IMAGE
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY FOLLOWED BY FLEXIBLE FITTING REFINEMENT PROTOCOL--MODELLED
RefinementHighest resolution: 8.5 Å
Refinement stepCycle: LAST / Highest resolution: 8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12404 0 0 0 12404

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