6WIM | pdb_00006wim

CdiB from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6WIM

This is version 1.2 of the entry. See complete history

Literature

Structural insight into toxin secretion by contact dependent growth inhibition transporters.

Guerin, J.Botos, I.Zhang, Z.Lundquist, K.Gumbart, J.C.Buchanan, S.K.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58100
  • Primary Citation Related Structures: 
    6WIL, 6WIM

  • PubMed Abstract: 

    Bacterial contact-dependent growth inhibition (CDI) systems use a type Vb secretion mechanism to export large CdiA toxins across the outer membrane by dedicated outer membrane transporters called CdiB. Here, we report the first crystal structures of two CdiB transporters from Acinetobacter baumannii and Escherichia coli . CdiB transporters adopt a TpsB fold, containing a 16-stranded transmembrane β-barrel connected to two periplasmic domains. The lumen of the CdiB pore is occluded by an N-terminal α-helix and the conserved extracellular loop 6; these two elements adopt different conformations in the structures. We identified a conserved DxxG motif located on strand β1 that connects loop 6 through different networks of interactions. Structural modifications of DxxG induce rearrangement of extracellular loops and alter interactions with the N-terminal α-helix, preparing the system for α-helix ejection. Using structural biology, functional assays, and molecular dynamics simulations, we show how the barrel pore is primed for CdiA toxin secretion.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States.

Macromolecule Content 

  • Total Structure Weight: 60.29 kDa 
  • Atom Count: 4,233 
  • Modeled Residue Count: 536 
  • Deposited Residue Count: 538 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane transporter CdiB538Escherichia coliMutation(s): 0 
Gene Names: cdiB
Membrane Entity: Yes 
UniProt
Find proteins for Q3YL97 (Escherichia coli)
Explore Q3YL97 
Go to UniProtKB:  Q3YL97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3YL97
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on PEG



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.953α = 90
b = 183.379β = 90
c = 45.324γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesOCI-1053575

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary