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- EMDB-48478: Cryo-EM of F-pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-48478
TitleCryo-EM of F-pilus
Map data
Sample
  • Complex: F-pilus
    • Protein or peptide: Pilin
  • Ligand: 1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE
KeywordsHelical / lipid / PROTEIN FIBRIL
Function / homologyTraA / TraA / extracellular region / plasma membrane / Pilin
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSonani RR / Francetic O / Lejeune M / Izadi-Pruneyre N / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: To Be Published
Title: Cryo-EM of F-pilus
Authors: Sonani RR
History
DepositionDec 26, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48478.png

Downloads & links

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Map

FileDownload / File: emd_48478.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 256 pix.
= 197.12 Å		0.77 Å/pix.
x 256 pix.
= 197.12 Å		0.77 Å/pix.
x 256 pix.
= 197.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2311039 - 0.41401362
Average (Standard dev.)0.0023872554 (±0.030504443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 197.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48478_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48478_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48478_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-pilus

EntireName: F-pilus
Components
  • Complex: F-pilus
    • Protein or peptide: Pilin
  • Ligand: 1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: F-pilus

SupramoleculeName: F-pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.780441 KDa
SequenceString:
MNAVLSVQGA SAPVKKKSFF SKFTRLNMLR LARAVIPAAV LMMFFPQLAM AAGSSGQDLM ASGNTTVKAT FGKDSSVVKW VVLAEVLVG AVMYMMTKNV KFLAGFAIIS VFIAVGMAVV GL

UniProtKB: Pilin

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Macromolecule #2: 1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: X41
Molecular weightTheoretical: 589.761 Da
Chemical component information

ChemComp-X41:
1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 13.366 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.094 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89344
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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