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- EMDB-52431: CryoEM structure of cyclised H-pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-52431
TitleCryoEM structure of cyclised H-pilus
Map datasharpened map
Sample
  • Organelle or cellular component: H-pilus
    • Protein or peptide: Pili assembly chaperone
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: water
KeywordsPilus / Conjugation / Filament / PROTEIN FIBRIL
Function / homologymembrane / Pili assembly chaperone
Function and homology information
Biological speciesSalmonella (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsIshimoto N / Beis K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cryoEM structure of H-pilus
Authors: Ishimoto N / Beis K
History
DepositionDec 26, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52431.png

Downloads & links

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Map

FileDownload / File: emd_52431.map.gz / Format: CCP4 / Size: 129.7 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.)
1.02 Å/pix.
x 324 pix.
= 330.48 Å		1.02 Å/pix.
x 324 pix.
= 330.48 Å		1.02 Å/pix.
x 324 pix.
= 330.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.58846295 - 1.151376
Average (Standard dev.)0.0029115144 (±0.054902025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 330.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52431_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_52431_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_52431_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H-pilus

EntireName: H-pilus
Components
  • Organelle or cellular component: H-pilus
    • Protein or peptide: Pili assembly chaperone
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: water

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Supramolecule #1: H-pilus

SupramoleculeName: H-pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella (bacteria)
Molecular weightTheoretical: 7.1 kDa/nm

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Macromolecule #1: Pili assembly chaperone

MacromoleculeName: Pili assembly chaperone / 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 (bacteria)
Molecular weightTheoretical: 7.601941 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSDDGAFGDI WAYMSEALTG APGKIIACGM LFSVAYFGVV KPNLGLALVS ALMMLVMANG EKIISSFLDA GIPL

UniProtKB: Pili assembly chaperone

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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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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 31 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / 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) / 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 / 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: 12.14 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.93 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123942
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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