8FAI

Cryo-EM structure of the Agrobacterium T-pilus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the Agrobacterium tumefaciens T4SS-associated T-pilus reveals stoichiometric protein-phospholipid assembly.

Kreida, S.Narita, A.Johnson, M.D.Tocheva, E.I.Das, A.Ghosal, D.Jensen, G.J.

(2023) Structure 31: 385-394.e4

  • DOI: https://doi.org/10.1016/j.str.2023.02.005
  • Primary Citation of Related Structures:  
    8FAI

  • PubMed Abstract: 

    Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an extracellular filament, the T-pilus, and is involved in mating pair formation between A. tumefaciens and the recipient plant cell. Here, we present a 3 Å cryoelectron microscopy (cryo-EM) structure of the T-pilus solved by helical reconstruction. Our structure reveals that the T-pilus is a stoichiometric assembly of the VirB2 major pilin and phosphatidylglycerol (PG) phospholipid with 5-start helical symmetry. We show that PG head groups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 abolished pilus formation. While our T-pilus structure is architecturally similar to previously published conjugative pili structures, the T-pilus lumen is narrower and positively charged, raising questions of whether the T-pilus is a conduit for ssDNA transfer.


  • Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein virB2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
121Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for P17792 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P17792 
Go to UniProtKB:  P17792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17792
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XL0 (Subject of Investigation/LOI)
Query on XL0

Download Ideal Coordinates CCD File 
AA [auth N]
BA [auth N]
CA [auth O]
DA [auth O]
P [auth F]
AA [auth N],
BA [auth N],
CA [auth O],
DA [auth O],
P [auth F],
Q [auth G],
R [auth H],
S [auth I],
T [auth J],
U [auth K],
V [auth K],
W [auth L],
X [auth L],
Y [auth M],
Z [auth M]
(7Z,19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacos-7-en-19-yl (9Z)-octadec-9-enoate
C40 H75 O10 P
VCYYBLIRAQBPTM-CTDKCSBDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONRELION4.0beta2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI127401
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1196924
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN 04345

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release