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- PDB-6h3l: Structure of VgrG1 in the Type VI secretion "pre-firing" VgrG1-Ts... -

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Basic information

Entry
Database: PDB / ID: 6h3l
TitleStructure of VgrG1 in the Type VI secretion "pre-firing" VgrG1-Tse6-EagT6-EF-Tu-Tsi6 complex
ComponentsVgrG1
KeywordsTOXIN / Bacterial Type VI effector complex / T6SS chaperone-effector complex / Tse6-loaded VgrG1 complex / NAD(P)+ Glycohydrolase
Function / homologyType VI secretion system, RhsGE-associated Vgr protein / Type VI secretion system, RhsGE-associated Vgr family subset / Vgr protein, OB-fold domain superfamily / Phage late control gene D protein (GPD) / type VI protein secretion system complex / protein secretion by the type VI secretion system / VgrG1
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsQuentin, D. / Raunser, S.
CitationJournal: Nat Microbiol / Year: 2018
Title: Mechanism of loading and translocation of type VI secretion system effector Tse6.
Authors: Dennis Quentin / Shehryar Ahmad / Premy Shanthamoorthy / Joseph D Mougous / John C Whitney / Stefan Raunser
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 19, 2018 / Release: Sep 12, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 12, 2018Structure modelrepositoryInitial release
1.1Oct 3, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: VgrG1
B: VgrG1
C: VgrG1


Theoretical massNumber of molelcules
Total (without water)216,2953
Polyers216,2953
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, electron cryo microscopy
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)46980
ΔGint (kcal/M)-178
Surface area (Å2)64150
MethodPISA

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Components

#1: Protein/peptide VgrG1


Mass: 72098.375 Da / Num. of mol.: 3
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: vgrG1, PA0091 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I741

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameDetailsEntity IDParent IDSource
1Type VI secretion "pre-firing" VgrG1-Tse6-EagT6-EF-Tu-Tsi6 complexThe type VI "pre-firing" complex consists of a single copy of Tse6, EF-Tu, Tsi6 and trimeric VgrG1 as well as two copies of dimeric EagT6.10RECOMBINANT
2Valine-glycine repeat protein 1VgrG1 forms a trimer - UniProt Identifier: Q9I74111RECOMBINANT
3Type VI secretion exported 6Tse6 - UniProt identifier: Q9I7391RECOMBINANT
4Type VI secretion immunity 6Tsi6 - UniProt identifier: Q9I7401RECOMBINANT
5Effector associated gene with tse6EagT6 forms dimers - UniProt identifier: Q9I738. Two dimers are present in the EM map.1RECOMBINANT
6Elongation factor Tu 1EF-Tu - UniProt identifier: P0CE471NATURAL
Molecular weight
IDValueEntity assembly IDExperimental value
10.35 MDa1NO
20.072 MDa1NO
30.045 MDa1NO
40.011 MDa1NO
50.016 MDa1NO
60.043 MDa1NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
32208964Pseudomonas aeruginosa PAO1 (bacteria)
43208964Pseudomonas aeruginosa PAO1 (bacteria)
54208964Pseudomonas aeruginosa PAO1 (bacteria)
65208964Pseudomonas aeruginosa PAO1 (bacteria)
76511693Escherichia coli BL21 (bacteria)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
32511693Escherichia coli BL21 (bacteria)
43511693Escherichia coli BL21 (bacteria)
54511693Escherichia coli BL21 (bacteria)
65511693Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTrisTris-HCl1
2300 mMsodium chlorideNaCl1
SpecimenConc.: 0.015 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 kelvins

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: 4200 nm / Nominal defocus min: 1700 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of real images: 11642
EM imaging opticsSph aberration corrector: Cs corrected microscope
Image scansMovie frames/image: 24

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Processing

EM software
IDNameVersionCategoryDetails
2EPU1.8image acquisition
12SPHIREclassificationsort3D
13SPHIRE3D reconstructionmeridien
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 55000 / Symmetry type: POINT

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