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- PDB-5ojq: The modeled structure of of wild type extended type VI secretion ... -

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Basic information

Entry
Database: PDB / ID: 5ojq
TitleThe modeled structure of of wild type extended type VI secretion system sheath/tube complex in vibrio cholerae based on cryo-EM reconstruction of the non-contractile sheath/tube complex
Components
  • Haemolysin co-regulated protein
  • Type VI secretion proteinType VI secretion system
  • VipA
KeywordsSTRUCTURAL PROTEIN / T6SS / extended conformation / vibrio cholerae / Structural protein
Function / homologyType VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system effector, Hcp / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Hcp1-like superfamily / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system effector, Hcp / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Uncharacterized protein / Type VI secretion protein / Haemolysin co-regulated protein ...Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system effector, Hcp / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Hcp1-like superfamily / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system effector, Hcp / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Uncharacterized protein / Type VI secretion protein / Haemolysin co-regulated protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.7 Å resolution
AuthorsWang, J. / Brackmann, M. / Castano-Diez, D. / Kudryashev, M. / Goldie, K. / Maier, T. / Stahlberg, H. / Basler, M.
CitationJournal: Nat Microbiol / Year: 2017
Title: Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Authors: Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 22, 2017 / Release: Aug 9, 2017

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Structure visualization

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Assembly

Deposited unit
1: Haemolysin co-regulated protein
A: Type VI secretion protein
2: Haemolysin co-regulated protein
B: Type VI secretion protein
3: Haemolysin co-regulated protein
C: Type VI secretion protein
4: Haemolysin co-regulated protein
D: Type VI secretion protein
5: Haemolysin co-regulated protein
E: Type VI secretion protein
6: Haemolysin co-regulated protein
F: Type VI secretion protein
a: VipA
G: VipA
H: VipA
I: VipA
J: VipA
K: VipA
L: Haemolysin co-regulated protein
X: Type VI secretion protein
N: Haemolysin co-regulated protein
Z: Type VI secretion protein
P: Haemolysin co-regulated protein
c: Type VI secretion protein
R: Haemolysin co-regulated protein
e: Type VI secretion protein
T: Haemolysin co-regulated protein
g: Type VI secretion protein
V: Haemolysin co-regulated protein
i: Type VI secretion protein
u: VipA
k: VipA
m: VipA
o: VipA
q: VipA
s: VipA
M: Haemolysin co-regulated protein
Y: Type VI secretion protein
O: Haemolysin co-regulated protein
b: Type VI secretion protein
Q: Haemolysin co-regulated protein
d: Type VI secretion protein
S: Haemolysin co-regulated protein
f: Type VI secretion protein
U: Haemolysin co-regulated protein
h: Type VI secretion protein
W: Haemolysin co-regulated protein
j: Type VI secretion protein
v: VipA
l: VipA
n: VipA
p: VipA
r: VipA
t: VipA


Theoretical massNumber of molelcules
Total (without water)1,610,67454
Polyers1,610,67454
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)389590
ΔGint (kcal/M)-2237
Surface area (Å2)567460
MethodPISA
Detailsdetails

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Components

#1: Protein/peptide
Haemolysin co-regulated protein / Hcp / Hcp1 family type VI secretion system effector / Type VI secretion system effector / Hcp1 family protein


Mass: 18878.055 Da / Num. of mol.: 18 / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: P72350
#2: Protein/peptide
Type VI secretion protein / Type VI secretion system / Type VI secretion system protein ImpC / VipB


Mass: 53504.434 Da / Num. of mol.: 18 / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: A0A085SGI6, UniProt: Q9KN57*PLUS
#3: Protein/peptide
VipA


Mass: 17099.416 Da / Num. of mol.: 18 / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: A0A023PRF3, UniProt: Q9KN58*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: T6SS extended sheath/tube complex / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Vibrio cholerae (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 23.5 deg. / Axial rise/subunit: 37.8 Å / Axial symmetry: C6
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10000 / Symmetry type: HELICAL

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