7W64

Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with N-terminal peptide fragment of TcpF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.

Oki, H.Kawahara, K.Iimori, M.Imoto, Y.Nishiumi, H.Maruno, T.Uchiyama, S.Muroga, Y.Yoshida, A.Yoshida, T.Ohkubo, T.Matsuda, S.Iida, T.Nakamura, S.

(2022) Sci Adv 8: eabo3013-eabo3013

  • DOI: https://doi.org/10.1126/sciadv.abo3013
  • Primary Citation of Related Structures:  
    7W63, 7W64, 7W65

  • PubMed Abstract: 

    Colonization of the host intestine is the most important step in Vibrio cholerae infection. The toxin-coregulated pilus (TCP), an operon-encoded type IVb pilus (T4bP), plays a crucial role in this process, which requires an additional secreted protein, TcpF, encoded on the same TCP operon; however, its mechanisms of secretion and function remain elusive. Here, we demonstrated that TcpF interacts with the minor pilin, TcpB, of TCP and elucidated the crystal structures of TcpB alone and in complex with TcpF. The structural analyses reveal how TCP recognizes TcpF and its secretory mechanism via TcpB-dependent pilus elongation and retraction. Upon binding to TCP, TcpF forms a flower-shaped homotrimer with its flexible N terminus hooked onto the trimeric interface of TcpB. Thus, the interaction between the minor pilin and the N terminus of the secreted protein, namely, the T4bP secretion signal, is key for V. cholerae colonization and is a new potential therapeutic target.


  • Organizational Affiliation

    Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin-coregulated pilus biosynthesis protein B
A, B, C, D, E
A, B, C, D, E, F
397Vibrio choleraeMutation(s): 0 
Gene Names: tcpB
UniProt
Find proteins for P23476 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P23476 
Go to UniProtKB:  P23476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23476
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TcpF
G, H, I, J, K
G, H, I, J, K, L
15Vibrio choleraeMutation(s): 0 
UniProt
Find proteins for P0C6Q5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6Q5 
Go to UniProtKB:  P0C6Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
R [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth F]
M [auth A]
O [auth B]
P [auth B]
Q [auth B]
AA [auth F],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth D],
W [auth E],
X [auth E],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth I]
DA [auth L]
N [auth A]
V [auth D]
BA [auth G],
CA [auth I],
DA [auth L],
N [auth A],
V [auth D],
Z [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.883α = 90
b = 128.555β = 90
c = 327.242γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K23866
Japan Society for the Promotion of Science (JSPS)Japan20K16245

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description