3KLO | pdb_00003klo

Vibrio cholerae VpsT bound to c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.290 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.246 (Depositor) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Vibrio cholerae VpsT Regulates Matrix Production and Motility by Directly Sensing Cyclic di-GMP.

Krasteva, P.V.Fong, J.C.Shikuma, N.J.Beyhan, S.Navarro, M.V.Yildiz, F.H.Sondermann, H.

(2010) Science 327: 866-868

  • DOI: https://doi.org/10.1126/science.1181185
  • Primary Citation Related Structures: 
    3KLN, 3KLO

  • PubMed Abstract: 

    Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.


  • Organizational Affiliation
    • Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

Macromolecule Content 

  • Total Structure Weight: 106.93 kDa 
  • Atom Count: 6,902 
  • Modeled Residue Count: 819 
  • Deposited Residue Count: 900 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator VpsT
A, B, C, D
225Vibrio cholerae O1 biovar El TorMutation(s): 0 
Gene Names: VCA0952VC_A0952
UniProt
Find proteins for Q9KKZ8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KKZ8 
Go to UniProtKB:  Q9KKZ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KKZ8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E

Query on C2E



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B],
H [auth C],
I [auth D]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
TAR

Query on TAR



Download:Ideal Coordinates CCD File
G [auth B],
J [auth D]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.290 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.246 (Depositor) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.703α = 90
b = 121.703β = 90
c = 208.227γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary