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- EMDB-56974: VgrG1 from Pseudomonas aeruginosa (PA0091) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56974
TitleVgrG1 from Pseudomonas aeruginosa (PA0091)
Map data
Sample
  • Complex: VgrG1 from Pseudomonas aeruginosa
    • Protein or peptide: Type VI secretion system spike protein VgrG1a
KeywordsType VI Secretion System / Homo-trimer / TOXIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsZimmermann M / Braun T
Funding support Switzerland, 1 items
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, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56974.png

Downloads & links

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Map

FileDownload / File: emd_56974.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.1338141 - 0.24031408
Average (Standard dev.)0.00007469817 (±0.006617195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56974_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56974_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56974_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : VgrG1 from Pseudomonas aeruginosa

EntireName: VgrG1 from Pseudomonas aeruginosa
Components
  • Complex: VgrG1 from Pseudomonas aeruginosa
    • Protein or peptide: Type VI secretion system spike protein VgrG1a

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Supramolecule #1: VgrG1 from Pseudomonas aeruginosa

SupramoleculeName: VgrG1 from Pseudomonas aeruginosa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Type VI secretion system spike protein VgrG1a

MacromoleculeName: Type VI secretion system spike protein VgrG1a / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 74.636281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLTRLVQVD CPLGPDVLLL QRMEGREELG RLFAYELHLV SENPNLPLEQ LLGKPMSLSL ELPGGSRRFF HGIVARCSQV AGHGQFAGY QATLRPWPWL LTRTSDCRIF QNQSVPEIIK QVFRNLGFSD FEDALTRPYR EWEYCVQYRE TSFDFISRLM E QEGIYYWF ...String:
MQLTRLVQVD CPLGPDVLLL QRMEGREELG RLFAYELHLV SENPNLPLEQ LLGKPMSLSL ELPGGSRRFF HGIVARCSQV AGHGQFAGY QATLRPWPWL LTRTSDCRIF QNQSVPEIIK QVFRNLGFSD FEDALTRPYR EWEYCVQYRE TSFDFISRLM E QEGIYYWF RHEQKRHILV LSDAYGAHRS PGGYASVPYY PPTLGHRERD HFFDWQMARE VQPGSLTLND YDFQRPGARL EV RSNIARP HAAADYPLYD YPGEYVQSQD GEQYARNRIE AIQAQHERVR LRGVVRGIGA GHLFRLSGYP RDDQNREYLV VGA EYRVVQ ELYETGSGGA GSQFESELDC IDASQSFRLL PQTPVPVVRG PQTAVVVGPK GEEIWTDQYG RVKVHFHWDR HDQS NENSS CWIRVSQAWA GKNWGSMQIP RIGQEVIVSF LEGDPDRPII TGRVYNAEQT VPYELPANAT QSGMKSRSSK GGTPA NFNE IRMEDKKGAE QLYIHAERNQ DNLVENDASL SVGHDRNKSI GHDELARIGN NRTRAVKLND TLLVGGAKSD SVTGTY LIE AGAQIRLVCG KSVVEFNADG TINISGSAFN LYASGNGNID TGGRLDLNSG GASEVDAKGK GVQGTIDGQV QAMFPPP AK GGSGESGSGR GVPHIVMVDA YKRYK

UniProtKB: Type VI secretion system spike protein VgrG1a

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris(hydroxymethyl)aminomethan
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Details: cryoWriter.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 1981 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 80000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab inito model
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 13092
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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