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- EMDB-65024: CryoEM structure of phospholipid-independent cyclised RP4 pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-65024
TitleCryoEM structure of phospholipid-independent cyclised RP4 pilus
Map datasharpened map
Sample
  • Organelle or cellular component: P-pilus
    • Protein or peptide: TrbC/VIRB2 family protein
KeywordsPilus / Conjugation / Antibiotic / PROTEIN FIBRIL
Function / homologyConjugal transfer TrbC/type IV secretion VirB2 / TrbC/VIRB2 pilin / TrbC/VIRB2 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsIshimoto N / Beis K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of phospholipid-independent cyclised RP4 pilu
Authors: Ishimoto N / Beis K
History
DepositionJun 10, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65024.png

Downloads & links

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Map

FileDownload / File: emd_65024.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 196 pix.
= 235.2 Å		1.2 Å/pix.
x 196 pix.
= 235.2 Å		1.2 Å/pix.
x 196 pix.
= 235.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.13348532 - 0.3068865
Average (Standard dev.)0.0023082865 (±0.019482369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 235.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65024_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map

Fileemd_65024_additional_1.map
Annotationmap
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_65024_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_65024_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : P-pilus

EntireName: P-pilus
Components
  • Organelle or cellular component: P-pilus
    • Protein or peptide: TrbC/VIRB2 family protein

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Supramolecule #1: P-pilus

SupramoleculeName: P-pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.14 kDa/nm

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Macromolecule #1: TrbC/VIRB2 family protein

MacromoleculeName: TrbC/VIRB2 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.139474 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SEGTGGSLPY ESWLTNLRNS VTGPVAFALS IIGIVVAGGV LIFGGELNAF FRTLIFLVLV MALLVGAQNV MSTFFGRG

UniProtKB: TrbC/VIRB2 family protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3405 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 15.15 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.62 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10674
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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