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

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Basic information

Entry
Database: PDB / ID: 5lfb
TitleStructure of the bacterial sex F pilus (12.5 Angstrom rise)
ComponentsPilin
KeywordsPROTEIN FIBRIL / F-pilus Conjugation Type IV secretion system Phospholipid
Function / homologyTraA / TraA / extracellular region / plasma membrane / Chem-6V6 / Pilin / Pilin
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5 Å
AuthorsCosta, T.R.D. / Ilangovan, I. / Ukleja, M. / Redzej, A. / Santini, J.M. / Smith, T.K. / Egelman, E.H. / Waksman, G.
Funding support United Kingdom, United States, 3items
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
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Revision 1.3Jan 31, 2018Group: Data processing / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1A: Pilin
1B: Pilin
1C: Pilin
1D: Pilin
1E: Pilin
1F: Pilin
1G: Pilin
1H: Pilin
1I: Pilin
1J: Pilin
1K: Pilin
1L: Pilin
1M: Pilin
1N: Pilin
1O: Pilin
2A: Pilin
2B: Pilin
2C: Pilin
2D: Pilin
2E: Pilin
2F: Pilin
2G: Pilin
2H: Pilin
2I: Pilin
2J: Pilin
2K: Pilin
2L: Pilin
2M: Pilin
2N: Pilin
2O: Pilin
3A: Pilin
3B: Pilin
3C: Pilin
3D: Pilin
3E: Pilin
3F: Pilin
3G: Pilin
3H: Pilin
3I: Pilin
3J: Pilin
3K: Pilin
3L: Pilin
3M: Pilin
3N: Pilin
3O: Pilin
4A: Pilin
4B: Pilin
4C: Pilin
4D: Pilin
4E: Pilin
4F: Pilin
4G: Pilin
4H: Pilin
4I: Pilin
4J: Pilin
4K: Pilin
4L: Pilin
4M: Pilin
4N: Pilin
4O: Pilin
5A: Pilin
5B: Pilin
5C: Pilin
5D: Pilin
5E: Pilin
5F: Pilin
5G: Pilin
5H: Pilin
5I: Pilin
5J: Pilin
5K: Pilin
5L: Pilin
5M: Pilin
5N: Pilin
5O: Pilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,413150
Polymers512,34175
Non-polymers54,07275
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Pilin


Mass: 6831.216 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B1VC86, UniProt: P04737*PLUS
#2: Chemical...
ChemComp-6V6 / [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate


Mass: 720.954 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: C38H73O10P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 7.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Lacey
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.67 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEM3.5.0image acquisition
4SPIDER22CTF correction
7Coot0.8.2model fitting
9PHENIXmodel refinement
10SPIDERinitial Euler assignment
11SPIDERfinal Euler assignment
12SPIDER22classification
13IHRSR3D reconstruction
14SPIDER223D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 28.1 ° / Axial rise/subunit: 12.5 Å / Axial symmetry: C5
3D reconstructionResolution: 5 Å / Resolution method: OTHER / Num. of particles: 16426 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

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