8S6H

Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the R388 plasmid conjugative pilus reveals a helical polymer characterized by an unusual pilin/phospholipid binary complex.

Vadakkepat, A.K.Xue, S.Redzej, A.Smith, T.K.Ho, B.T.Waksman, G.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.06.009
  • Primary Citation of Related Structures:  
    8S6H

  • PubMed Abstract: 

    Bacterial conjugation is a process by which DNA is transferred unidirectionally from a donor cell to a recipient cell. It is the main means by which antibiotic resistance genes spread among bacterial populations. It is crucially dependent upon the elaboration of an extracellular appendage, termed "pilus," by a large double-membrane-spanning secretion system termed conjugative "type IV secretion system." Here we present the structure of the conjugative pilus encoded by the R388 plasmid. We demonstrate that, as opposed to all conjugative pili produced so far for cryoelectron microscopy (cryo-EM) structure determination, the conjugative pilus encoded by the R388 plasmid is greatly stimulated by the presence of recipient cells. Comparison of its cryo-EM structure with existing conjugative pilus structures highlights a number of important differences between the R388 pilus structure and that of its homologs, the most prominent being the highly distinctive conformation of its bound lipid.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK. Electronic address: akv10@leicester.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TrwL protein69Escherichia coli HB101Mutation(s): 0 
UniProt
Find proteins for O50328 (Escherichia coli)
Explore O50328 
Go to UniProtKB:  O50328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50328
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LHG (Subject of Investigation/LOI)
Query on LHG

Download Ideal Coordinates CCD File 
AC [auth L]
AD [auth r]
AE [auth S]
BC [auth L]
BD [auth s]
AC [auth L],
AD [auth r],
AE [auth S],
BC [auth L],
BD [auth s],
BE [auth U],
CC [auth M],
CD [auth t],
CE [auth V],
DC [auth M],
DD [auth u],
DE [auth W],
EC [auth 3],
ED [auth v],
EE [auth W],
FC [auth 4],
FD [auth v],
FE [auth X],
GC [auth 4],
GD [auth x],
GE [auth Y],
HC [auth 5],
HD [auth z],
HE [auth Z],
IC [auth 6],
ID [auth c],
JC [auth 8],
JD [auth c],
KC [auth 8],
KD [auth d],
LC [auth 9],
LD [auth f],
MC [auth A1],
MD [auth h],
NC [auth A2],
ND [auth i],
OC [auth A2],
OD [auth i],
PC [auth A3],
PD [auth j],
QC [auth A4],
QD [auth j],
RB [auth A],
RC [auth A5],
RD [auth k],
SB [auth B],
SC [auth A6],
SD [auth O],
TB [auth B],
TC [auth A6],
TD [auth O],
UB [auth D],
UC [auth 0],
UD [auth P],
VB [auth E],
VC [auth 1],
VD [auth P],
WB [auth F],
WC [auth 1],
WD [auth Q],
XB [auth I],
XC [auth 2],
XD [auth R],
YB [auth J],
YC [auth p],
YD [auth R],
ZB [auth K],
ZC [auth q],
ZD [auth S]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCCRYOSPARC v4.3.1
MODEL REFINEMENTPHENIX1.21rc1_5058

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom217089

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release