2XMN

High resolution snapshots of defined TolC open states present an iris- like movement of periplasmic entrance helices


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structures of sequential open states in a symmetrical opening transition of the TolC exit duct.

Pei, X.Y.Hinchliffe, P.Symmons, M.F.Koronakis, E.Benz, R.Hughes, C.Koronakis, V.

(2011) Proc Natl Acad Sci U S A 108: 2112-2117

  • DOI: https://doi.org/10.1073/pnas.1012588108
  • Primary Citation of Related Structures:  
    2WMZ, 2XMN

  • PubMed Abstract: 

    In bacterial drug resistance and virulence pumps, an inner membrane (IM) transporter and periplasmic adaptor recruit an outer membrane (OM) trimeric TolC exit duct that projects an α-helical tunnel across the periplasm. The TolC periplasmic entrance is closed by densely packed α-helical coiled coils, inner H7/H8, and outer H3/H4, constrained by a hydrogen bond network. On recruitment, these coiled coils must undergo transition to the open state. We present 2.9 Å resolution crystal structures of two sequential TolC open states in which the network is incrementally disrupted and channel conductances defined in lipid bilayers. Superimposition of TolC(RS) (370 pS) and TolC(YFRS) (1,000 pS) on the TolC(WT) closed state (80 pS) showed that in the initial open-state TolC(RS), relaxation already causes approximately 14° twisting and expansion of helix H7 at the periplasmic tip, increasing interprotomer distances from 12.2 Å in TolC(WT) to 18.9 Å. However, in the crystal structure, the weakened Asp(374) pore constriction was maintained at the closed state 11.3 Å(2). In the advanced open-state TolC(YFRS), there was little further expansion at the tip, to interprotomer 21.3 Å, but substantial movement of inner and outer coiled coils dilated the pore constriction. In particular, upon abolition of the TolC(YFRS) intraprotomer Tyr(362)-Asp(153) link, a redirection of Tyr(362) and "bulge" in H3 allowed a simple movement outward of H8, establishing a 50.3 Å(2) opening. Root mean square deviations (rmsds) over the coiled coils of the three protomers of TolC(RS) and TolC(YFRS) illustrate that, whereas independent movement at the periplasmic tips may feature in the initial stages of opening, full dilation of the pore constriction is entirely symmetrical.


  • Organizational Affiliation

    Department of Pathology, Cambridge University, Cambridge CB2 1QP, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein TolC
A, B, C
428Escherichia coli K-12Mutation(s): 2 
Gene Names: tolCcolE1-imtcBmukArefItocweeAb3035JW5503
Membrane Entity: Yes 
UniProt
Find proteins for P02930 (Escherichia coli (strain K12))
Explore P02930 
Go to UniProtKB:  P02930
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02930
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.124α = 90
b = 135.524β = 90
c = 136.343γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-09-19
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description