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- EMDB-4046: Cryo-EM structure of the bacterial sex F pilus (12.5 Angstrom rise) -

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Basic information

Entry
Database: EMDB / ID: EMD-4046
TitleCryo-EM structure of the bacterial sex F pilus (12.5 Angstrom rise)
Map data
Sample
  • Organelle or cellular component: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex
    • Protein or peptide: Pilin
  • Ligand: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate
KeywordsF-pilus Conjugation Type IV secretion system Phospholipid / Protein fibril
Function / homologyTraA / TraA / extracellular region / plasma membrane / Pilin / Pilin
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsCosta TRD / Ilangovan I
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust093228 United Kingdom
National Institutes of HealthGM035269 United States
CitationJournal: Cell / Year: 2016
Title: Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex.
Authors: Tiago R D Costa / Aravindan Ilangovan / Marta Ukleja / Adam Redzej / Joanne M Santini / Terry K Smith / Edward H Egelman / Gabriel Waksman /
Abstract: Conjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among ...Conjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among conjugative pili, the F "sex" pilus encoded by the F plasmid is the best functionally characterized, and it is also historically the most important, as the discovery of F-plasmid-mediated conjugation ushered in the era of molecular biology and genetics. Yet, its structure is unknown. Here, we present atomic models of two F family pili, the F and pED208 pili, generated from cryoelectron microscopy reconstructions at 5.0 and 3.6 Å resolution, respectively. These structures reveal that conjugative pili are assemblies of stoichiometric protein-phospholipid units. We further demonstrate that each pilus type binds preferentially to particular phospholipids. These structures provide the molecular basis for F pilus assembly and also shed light on the remarkable properties of conjugative pili in bacterial secretion and phage infection.
History
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
DepositionOct 18, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 44
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lfb
  • Surface level: 44
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5lfb
  • Surface level: 44
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lfb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4046.png

Downloads & links

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Map

FileDownload / File: emd_4046.map.gz / Format: CCP4 / Size: 16 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 128 pix.
= 140.8 Å		1.1 Å/pix.
x 128 pix.
= 140.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 44.0 / Movie #1: 44
Minimum - Maximum-40.861893000000002 - 145.205659999999995
Average (Standard dev.)6.742356 (±19.043503000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128256
Spacing128128256
CellA: 140.8 Å / B: 140.8 Å / C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z128128256
origin x/y/z0.0000.0000.000
length x/y/z140.800140.800281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128256
D min/max/mean-40.862145.2066.742

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Supplemental data

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Sample components

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Entire : F-pilus filament made by an assembly of a stoichiometric protein-...

EntireName: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex
Components
  • Organelle or cellular component: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex
    • Protein or peptide: Pilin
  • Ligand: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate

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Supramolecule #1: F-pilus filament made by an assembly of a stoichiometric protein-...

SupramoleculeName: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.3 kDa/nm

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 75 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.831216 KDa
SequenceString:
QDLMASGNTT VKATFGKDSS VVKWVVLAEV LVGAVMYMMT KNVKFLAGFA IISVFIAVGM AVVGL

UniProtKB: Pilin

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Macromolecule #2: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...

MacromoleculeName: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate
type: ligand / ID: 2 / Number of copies: 75 / Formula: 6V6
Molecular weightTheoretical: 720.954 Da
Chemical component information

ChemComp-6V6:
[(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
GridModel: Lacey / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 12.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.1 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: OTHER / Software: (Name: IHRSR, SPIDER (ver. 22)) / Number images used: 16426
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-5lfb:
Structure of the bacterial sex F pilus (12.5 Angstrom rise)

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