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- PDB-5myu: VipA-N2/VipB contracted sheath of type VI secretion system -

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Basic information

Entry
Database: PDB / ID: 5myu
TitleVipA-N2/VipB contracted sheath of type VI secretion system
Components
  • Type VI secretion system protein ImpCType VI secretion system
  • Uncharacterized protein
KeywordsPROTEIN TRANSPORT / Bacterial type VI secretion system / protein export / protein transport
Function / homologyType VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Uncharacterized protein / Type VI secretion protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4 Å resolution
AuthorsWang, J. / Brackmann, B. / Castano-Diez, D. / Kudryashev, M. / Goldie, D. / 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: Jan 27, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Nov 8, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
a: Uncharacterized protein
A: Type VI secretion system protein ImpC
b: Uncharacterized protein
B: Type VI secretion system protein ImpC
c: Uncharacterized protein
C: Type VI secretion system protein ImpC
d: Uncharacterized protein
D: Type VI secretion system protein ImpC
e: Uncharacterized protein
E: Type VI secretion system protein ImpC
f: Uncharacterized protein
F: Type VI secretion system protein ImpC


Theoretical massNumber of molelcules
Total (without water)377,31112
Polyers377,31112
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)52000
ΔGint (kcal/M)-348
Surface area (Å2)174120
MethodPISA

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Components

#1: Protein/peptide
Uncharacterized protein


Mass: 13916.752 Da / Num. of mol.: 6 / Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A023PRF3, UniProt: Q9KN58*PLUS
#2: Protein/peptide
Type VI secretion system protein ImpC / Type VI secretion system / Uncharacterized protein ImpC


Mass: 48968.332 Da / Num. of mol.: 6 / Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ERS013138_01484, ERS013140_01660, ERS013165_01090, ERS013186_01572, ERS013198_01471, ERS013199_00294, ERS013200_00406, ERS013201_01395, ERS013202_00755, ERS013206_01101, ERS013207_02465
Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A023PTI7, UniProt: Q9KN57*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: Type IV secretion system sheath-tubeSecretion / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2 / 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: 30 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: 29.4 deg. / Axial rise/subunit: 21.7 Å / Axial symmetry: C6
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7000 / Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingRef protocol: RIGID BODY FIT

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