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- PDB-28yn: VgrG1 from Pseudomonas aeruginosa (PA0091) -

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Basic information

Entry
Database: PDB / ID: 28yn
TitleVgrG1 from Pseudomonas aeruginosa (PA0091)
ComponentsType VI secretion system spike protein VgrG1a
KeywordsTOXIN / Type VI Secretion System / Homo-trimer
Function / homology
Function and homology information


protein secretion by the type VI secretion system / type VI protein secretion system complex / extracellular region
Similarity search - Function
: / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / :
Similarity search - Domain/homology
Type VI secretion system spike protein VgrG1a
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsZimmermann, M. / Braun, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Biorxiv / Year: 2026
Title: Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material
Authors: Zimmermann, M. / Braun, T.
History
DepositionMar 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type VI secretion system spike protein VgrG1a
B: Type VI secretion system spike protein VgrG1a
C: Type VI secretion system spike protein VgrG1a


Theoretical massNumber of molelcules
Total (without water)223,9093
Polymers223,9093
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Type VI secretion system spike protein VgrG1a / T6SS spike protein VgrG1a


Mass: 74636.281 Da / Num. of mol.: 3 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: vgrG1a, PA0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I741
Has protein modificationN

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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: VgrG1 from Pseudomonas aeruginosa / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethanC4H11NO31
2150 mMSodium ChlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Details: cryoWriter

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1981
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2EPUimage acquisition
4cryoSPARC4.7.1CTF correction
7UCSF ChimeraX1.11.1model fitting
9cryoSPARC4.7.1initial Euler assignment
10cryoSPARC4.7.1final Euler assignment
12cryoSPARC4.7.13D reconstruction
13PHENIX2model refinement
14Coot1.1.15model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 80000
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13092 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 73.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002615594
ELECTRON MICROSCOPYf_angle_d0.504821132
ELECTRON MICROSCOPYf_chiral_restr0.0452184
ELECTRON MICROSCOPYf_plane_restr0.00422853
ELECTRON MICROSCOPYf_dihedral_angle_d5.01232174

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