5LER

Structure of the bacterial sex F pilus (13.2 Angstrom rise)

• PDB DOI:  https://doi.org/10.2210/pdb5LER/pdb
• EM Map EMD-4044: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-30 Released: 2016-11-02 
• Deposition Author(s): Costa, T.R.D., Ilangovan, I., Ukleja, M., Redzej, A., Santini, J.M., Smith, T.K., Egelman, E.H., Waksman, G.
• Funding Organization(s): Wellcome Trust, National Institutes of Health

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex.

Costa, T.R., Ilangovan, A., Ukleja, M., Redzej, A., Santini, J.M., Smith, T.K., Egelman, E.H., Waksman, G.

(2016) Cell 166: 1436-1444.e10

• PubMed: 27610568 
• DOI: https://doi.org/10.1016/j.cell.2016.08.025
• Primary Citation of Related Structures:  
  5LEG, 5LER, 5LFB


• PubMed 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, 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.

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 75-mer - A75 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 562.81 kDa 
• Atom Count: 36,539 
• Modelled Residue Count: 4,875 
• Deposited Residue Count: 4,875 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pilin	A [auth 1A], AA [auth 2L], AB [auth 4H], B [auth 1B], BA [auth 2M], BB [auth 4I], C [auth 1C], CA [auth 2N], CB [auth 4J], D [auth 1D], DA [auth 2O], DB [auth 4K], E [auth 1E], EA [auth 3A], EB [auth 4L], F [auth 1F], FA [auth 3B], FB [auth 4M], G [auth 1G], GA [auth 3C], GB [auth 4N], H [auth 1H], HA [auth 3D], HB [auth 4O], I [auth 1I], IA [auth 3E], IB [auth 5A], J [auth 1J], JA [auth 3F], JB [auth 5B], K [auth 1K], KA [auth 3G], KB [auth 5C], L [auth 1L], LA [auth 3H], LB [auth 5D], M [auth 1M], MA [auth 3I], MB [auth 5E], N [auth 1N], NA [auth 3J], NB [auth 5F], O [auth 1O], OA [auth 3K], OB [auth 5G], P [auth 2A], PA [auth 3L], PB [auth 5H], Q [auth 2B], QA [auth 3M], QB [auth 5I], R [auth 2C], RA [auth 3N], RB [auth 5J], S [auth 2D], SA [auth 3O], SB [auth 5K], T [auth 2E], TA [auth 4A], TB [auth 5L], U [auth 2F], UA [auth 4B], UB [auth 5M], V [auth 2G], VA [auth 4C], VB [auth 5N], W [auth 2H], WA [auth 4D], WB [auth 5O], X [auth 2I], XA [auth 4E], Y [auth 2J], YA [auth 4F], Z [auth 2K], ZA [auth 4G]	65	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P04737 (Escherichia coli (strain K12)) Explore P04737  Go to UniProtKB:  P04737

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6V6	AC [auth 1D], AD [auth 3B], AE [auth 4N], BC [auth 1E], BD [auth 3C], BE [auth 5A], CC [auth 1F], CD [auth 3D], CE [auth 5B], DC [auth 1G], DD [auth 3E], DE [auth 5C], EC [auth 1H], ED [auth 3F], EE [auth 5D], FC [auth 1I], FD [auth 3G], FE [auth 5E], GC [auth 1J], GD [auth 3H], GE [auth 5F], HC [auth 1K], HD [auth 3I], HE [auth 5G], IC [auth 1L], ID [auth 3J], IE [auth 5H], JC [auth 1M], JD [auth 3K], JE [auth 5I], KC [auth 1N], KD [auth 3L], KE [auth 5J], LC [auth 2A], LD [auth 3M], LE [auth 5K], MC [auth 2B], MD [auth 3N], ME [auth 5L], NC [auth 2C], ND [auth 4A], NE [auth 5M], OC [auth 2D], OD [auth 4B], OE [auth 5N], PC [auth 2E], PD [auth 4C], QC [auth 2F], QD [auth 4D], RC [auth 2G], RD [auth 4E], SC [auth 2H], SD [auth 4F], TC [auth 2I], TD [auth 4G], UC [auth 2J], UD [auth 4H], VC [auth 2K], VD [auth 4I], WC [auth 2L], WD [auth 4J], XB [auth 1A], XC [auth 2M], XD [auth 4K], YB [auth 1B], YC [auth 2N], YD [auth 4L], ZB [auth 1C], ZC [auth 3A], ZD [auth 4M]	[(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate C38 H73 O10 P NOFOTAHTYLXZNV-RERZGLEZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10.1-2155
RECONSTRUCTION	IHRSR
RECONSTRUCTION	SPIDER	22

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Costa, T.R.D., Ilangovan, I., Ukleja, M., Redzej, A., Santini, J.M., Smith, T.K., Egelman, E.H., Waksman, G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098302
Wellcome Trust	United Kingdom	093228
National Institutes of Health	United States	GM035269

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Data collection
• Version 1.2: 2017-08-30
  Changes: Data collection
• Version 1.3: 2018-01-31
  Changes: Data processing