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- PDB-3zbi: Fitting result in the O-layer of the subnanometer structure of th... -

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Basic information

Entry
Database: PDB / ID: 3zbi
TitleFitting result in the O-layer of the subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
Components
  • TRAF PROTEINTNF receptor associated factor
  • TRAN PROTEIN
  • TRAO PROTEIN
KeywordsCELL ADHESION / BACTERIAL SECRETION
Function / homology
Function and homology information


: / P-type Type IV secretion system, TraN / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
TraN protein / TraO protein / TraF protein
Similarity search - Component
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.
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 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Dec 14, 2016Group: Other
Revision 1.3Aug 23, 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
  • Imaged by Jmol
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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: TRAF PROTEIN
B: TRAO PROTEIN
C: TRAN PROTEIN
D: TRAF PROTEIN
E: TRAO PROTEIN
F: TRAN PROTEIN
G: TRAF PROTEIN
H: TRAO PROTEIN
I: TRAN PROTEIN
J: TRAF PROTEIN
K: TRAO PROTEIN
L: TRAN PROTEIN
M: TRAF PROTEIN
N: TRAO PROTEIN
O: TRAN PROTEIN
P: TRAF PROTEIN
Q: TRAO PROTEIN
R: TRAN PROTEIN
S: TRAF PROTEIN
T: TRAO PROTEIN
U: TRAN PROTEIN
V: TRAF PROTEIN
W: TRAO PROTEIN
X: TRAN PROTEIN
Y: TRAF PROTEIN
Z: TRAO PROTEIN
a: TRAN PROTEIN
b: TRAF PROTEIN
c: TRAO PROTEIN
d: TRAN PROTEIN
e: TRAF PROTEIN
f: TRAO PROTEIN
g: TRAN PROTEIN
h: TRAF PROTEIN
i: TRAO PROTEIN
j: TRAN PROTEIN
k: TRAF PROTEIN
l: TRAO PROTEIN
m: TRAN PROTEIN
n: TRAF PROTEIN
o: TRAO PROTEIN
p: TRAN PROTEIN


Theoretical massNumber of molelcules
Total (without water)598,90742
Polymers598,90742
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
TRAF PROTEIN / TNF receptor associated factor


Mass: 22962.553 Da / Num. of mol.: 14 / Fragment: C-TERMINAL DOMAIN, RESIDUES 171-386
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: Q46705
#2: Protein
TRAO PROTEIN


Mass: 14680.648 Da / Num. of mol.: 14 / Fragment: C-TERMINAL DOMAIN, RESIDUES 161-290
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
#3: Protein/peptide
TRAN PROTEIN


Mass: 5135.873 Da / Num. of mol.: 14
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: Q46702

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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--X-RAY
Atomic model buildingPDB-ID: 3JQO

3jqo

RefinementHighest resolution: 8.5 Å
Refinement stepCycle: LAST / Highest resolution: 8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37884 0 0 0 37884

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