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- PDB-3j9g: Atomic model of the VipA/VipB, the type six secretion system cont... -

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Basic information

Entry
Database: PDB / ID: 3j9g
TitleAtomic model of the VipA/VipB, the type six secretion system contractile sheath of Vibrio cholerae from cryo-EM
Components
  • VipAVirtually imaged phased array
  • VipB
KeywordsCONTRACTILE PROTEIN / t6ss / bacterial secretion / phage / contraction
Function / homologyType VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKudryashev, M. / Wang, R.Y.-R. / Brackmann, M. / Scherer, S. / Maier, T. / Baker, D. / DiMaio, F. / Stahlberg, H. / Egelman, E.H. / Basler, M.
CitationJournal: Cell / Year: 2015
Title: Structure of the type VI secretion system contractile sheath.
Authors: Mikhail Kudryashev / Ray Yu-Ruei Wang / Maximilian Brackmann / Sebastian Scherer / Timm Maier / David Baker / Frank DiMaio / Henning Stahlberg / Edward H Egelman / Marek Basler /
Abstract: Bacteria use rapid contraction of a long sheath of the type VI secretion system (T6SS) to deliver effectors into a target cell. Here, we present an atomic-resolution structure of a native contracted ...Bacteria use rapid contraction of a long sheath of the type VI secretion system (T6SS) to deliver effectors into a target cell. Here, we present an atomic-resolution structure of a native contracted Vibrio cholerae sheath determined by cryo-electron microscopy. The sheath subunits, composed of tightly interacting proteins VipA and VipB, assemble into a six-start helix. The helix is stabilized by a core domain assembled from four β strands donated by one VipA and two VipB molecules. The fold of inner and middle layers is conserved between T6SS and phage sheaths. However, the structure of the outer layer is distinct and suggests a mechanism of interaction of the bacterial sheath with an accessory ATPase, ClpV, that facilitates multiple rounds of effector delivery. Our results provide a mechanistic insight into assembly of contractile nanomachines that bacteria and phages use to translocate macromolecules across membranes.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2699
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VipA
B: VipB
C: VipA
D: VipB
E: VipA
F: VipB
G: VipA
H: VipB
I: VipA
J: VipB
K: VipA
L: VipB
M: VipA
N: VipB
O: VipA
P: VipB
Q: VipA
R: VipB
S: VipA
T: VipB
U: VipA
V: VipB
W: VipA
X: VipB
Y: VipA
Z: VipB
a: VipA
b: VipB
c: VipA
d: VipB
e: VipA
f: VipB
g: VipA
h: VipB
i: VipA
j: VipB
k: VipA
l: VipB
m: VipA
n: VipB
o: VipA
p: VipB
q: VipA
r: VipB
s: VipA
t: VipB
u: VipA
v: VipB
w: VipA
x: VipB
y: VipA
z: VipB
1: VipA
2: VipB
3: VipA
4: VipB
5: VipA
6: VipB
7: VipA
8: VipB


Theoretical massNumber of molelcules
Total (without water)1,886,52360
Polymers1,886,52360
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 21.8 Å / Rotation per n subunits: 29.4 °)

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Components

#1: Protein ...
VipA / Virtually imaged phased array


Mass: 13716.561 Da / Num. of mol.: 30 / Fragment: UNP residues 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0107 / Production host: Vibrio cholerae 2740-80 (bacteria) / References: UniProt: Q9KN58
#2: Protein ...
VipB


Mass: 49167.539 Da / Num. of mol.: 30 / Fragment: UNP residues 61-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0108 / Production host: Vibrio cholerae 2740-80 (bacteria) / References: UniProt: Q9KN57

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1Vibrio cholerae VipA/VipB sheath in a contracted stateCOMPLEX0
2VipAVirtually imaged phased array1
3VipB1
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon grids, Quantifoil 1.2/1.3, imaged over the holes
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 77 K / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV) / Method: plunge freezing

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 15, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 63 K / Tilt angle max: 5 ° / Tilt angle min: -5 °
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) / Details: Operated in counting non-superresolution mode
Image scansNum. digital images: 72

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Processing

EM software
IDNameCategory
1CTFFINDCTF correction
2Helixboxerparticle selection
3IHRSR3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: Phase Flip, CTF detection by CTFFIND
Helical symmertyAngular rotation/subunit: 29.4 ° / Axial rise/subunit: 21.8 Å / Axial symmetry: C6
3D reconstructionMethod: Iterative Real Space Helical Reconstruction / Resolution: 3.5 Å / Num. of particles: 96000 / Nominal pixel size: 0.5 Å / Actual pixel size: 0.5 Å
Magnification calibration: Magnification was calibrated in the microscope using a gold lattice.
Num. of class averages: 1 / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms132930 0 0 0 132930

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