2X79 | pdb_00002x79

Inward facing conformation of Mhp1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.313 (Depositor), 0.331 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.297 (DCC) 
  • R-Value Observed: 
    0.277 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1.

Shimamura, T.Weyand, S.Beckstein, O.Rutherford, N.G.Hadden, J.M.Sharples, D.Sansom, M.S.P.Iwata, S.Henderson, P.J.F.Cameron, A.D.

(2010) Science 328: 470

  • DOI: https://doi.org/10.1126/science.1186303
  • Primary Citation Related Structures: 
    2X79

  • PubMed Abstract: 

    The structure of the sodium-benzylhydantoin transport protein Mhp1 from Microbacterium liquefaciens comprises a five-helix inverted repeat, which is widespread among secondary transporters. Here, we report the crystal structure of an inward-facing conformation of Mhp1 at 3.8 angstroms resolution, complementing its previously described structures in outward-facing and occluded states. From analyses of the three structures and molecular dynamics simulations, we propose a mechanism for the transport cycle in Mhp1. Switching from the outward- to the inward-facing state, to effect the inward release of sodium and benzylhydantoin, is primarily achieved by a rigid body movement of transmembrane helices 3, 4, 8, and 9 relative to the rest of the protein. This forms the basis of an alternating access mechanism applicable to many transporters of this emerging superfamily.


  • Organizational Affiliation
    • Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK.

Macromolecule Content 

  • Total Structure Weight: 55.56 kDa 
  • Atom Count: 3,585 
  • Modeled Residue Count: 465 
  • Deposited Residue Count: 501 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hydantoin permease501Microbacterium maritypicumMutation(s): 0 
Gene Names: hyuP
Membrane Entity: Yes 
UniProt
Find proteins for D6R8X8 (Microbacterium maritypicum)
Explore D6R8X8 
Go to UniProtKB:  D6R8X8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6R8X8
Sequence Annotations
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Reference Sequence

Small Molecules

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: 3.80 Å
  • R-Value Free:  0.313 (Depositor), 0.331 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.297 (DCC) 
  • R-Value Observed: 0.277 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.888α = 90
b = 173.888β = 90
c = 74.502γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    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: 2024-05-08
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-09-11
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Structure summary