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- EMDB-65234: CryoEM structure of cyclised H-pilus (D69A) -

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Basic information

Entry
Database: EMDB / ID: EMD-65234
TitleCryoEM structure of cyclised H-pilus (D69A)
Map datasharpening map
Sample
  • Organelle or cellular component: Pilus (D69A)
    • Protein or peptide: Pilin
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Keywordspilus / conjugation / filament / PROTEIN FIBRIL
Function / homologymembrane / Pilin
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria) / Salmonella enterica subsp. enterica serovar Typhi
Methodhelical reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsIshimoto N / Beis K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Surface electrostatic potential affects mating pilus functionality
Authors: He S / Ishimoto N / Wong J / David S / Beis K / Frankel G
History
DepositionJul 2, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65234.png

Downloads & links

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Map

FileDownload / File: emd_65234.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.6538645 - 1.1406245
Average (Standard dev.)0.003277436 (±0.060457528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65234_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map

Fileemd_65234_additional_1.map
Annotationmap
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_65234_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_65234_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pilus (D69A)

EntireName: Pilus (D69A)
Components
  • Organelle or cellular component: Pilus (D69A)
    • Protein or peptide: Pilin
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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Supramolecule #1: Pilus (D69A)

SupramoleculeName: Pilus (D69A) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Molecular weightTheoretical: 7.1 kDa/nm

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1
Details: The last five residues of AGIPL are cleaved when H-pilus make cyclisation.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi
Molecular weightTheoretical: 7.557932 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSDDGAFGDI WAYMSEALTG APGKIIACGM LFSVAYFGVV KPNLGLALVS ALMMLVMANG EKIISSFLAA GIPL

UniProtKB: Pilin

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Macromolecule #2: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 2 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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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 / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 12.24 Å
Applied symmetry - Helical parameters - Δ&Phi: 29.00 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 420903
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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