2YNK | pdb_00002ynk

Wzi, an Outer Membrane Protein Involved in Group 1 Capsule Assembly in Escherichia coli, is a Carbohydrate Binding Beta-Barrel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.279 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2YNK

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Wzi is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia Coli.

Bushell, S.R.Mainprize, I.L.Wear, M.A.Lou, H.Whitfield, C.Naismith, J.H.

(2013) Structure 21: 844

  • DOI: https://doi.org/10.1016/j.str.2013.03.010
  • Primary Citation Related Structures: 
    2YNK

  • PubMed Abstract: 

    Many pathogenic bacteria encase themselves in a polysaccharide capsule that provides a barrier to the physical and immunological challenges of the host. The mechanism by which the capsule assembles around the bacterial cell is unknown. Wzi, an integral outer-membrane protein from Escherichia coli, has been implicated in the formation of group 1 capsules. The 2.6 Å resolution structure of Wzi reveals an 18-stranded β-barrel fold with a novel arrangement of long extracellular loops that blocks the extracellular entrance and a helical bundle that plugs the periplasmic end. Mutagenesis shows that specific extracellular loops are required for in vivo capsule assembly. The data show that Wzi binds the K30 carbohydrate polymer and, crucially, that mutants functionally deficient in vivo show no binding to K30 polymer in vitro. We conclude that Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.


  • Organizational Affiliation
    • Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK.

Macromolecule Content 

  • Total Structure Weight: 53.4 kDa 
  • Atom Count: 3,652 
  • Modeled Residue Count: 441 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WZI456Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q8GNN6 (Escherichia coli)
Explore Q8GNN6 
Go to UniProtKB:  Q8GNN6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GNN6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D12

Query on D12



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
B [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
B [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX

Query on HEX



Download:Ideal Coordinates CCD File
N [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.279 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.66α = 90
b = 152.08β = 90
c = 95.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary