4LLH

Substrate bound outward-open state of the symporter BetP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na(+) coupling.

Perez, C.Faust, B.Mehdipour, A.R.Francesconi, K.A.Forrest, L.R.Ziegler, C.

(2014) Nat Commun 5: 4231-4231

  • DOI: https://doi.org/10.1038/ncomms5231
  • Primary Citation of Related Structures:  
    4LLH

  • PubMed Abstract: 

    The Na(+)-coupled betaine symporter BetP shares a highly conserved fold with other sequence unrelated secondary transporters, for example, with neurotransmitter symporters. Recently, we obtained atomic structures of BetP in distinct conformational states, which elucidated parts of its alternating-access mechanism. Here, we report a structure of BetP in a new outward-open state in complex with an anomalous scattering substrate, adding a fundamental piece to an unprecedented set of structural snapshots for a secondary transporter. In combination with molecular dynamics simulations these structural data highlight important features of the sequential formation of the substrate and sodium-binding sites, in which coordinating water molecules play a crucial role. We observe a strictly interdependent binding of betaine and sodium ions during the coupling process. All three sites undergo progressive reshaping and dehydration during the alternating-access cycle, with the most optimal coordination of all substrates found in the closed state.


  • Organizational Affiliation

    1] Structural Biology Department, Max-Planck Institute of Biophysics, Frankfurt am Main 60438, Germany [2] [3].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine betaine transporter BetP
A, B, C
566Corynebacterium glutamicum ATCC 13032Mutation(s): 1 
Gene Names: betPCgl0892cg1016
Membrane Entity: Yes 
UniProt
Find proteins for P54582 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore P54582 
Go to UniProtKB:  P54582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54582
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CM5
Query on CM5

Download Ideal Coordinates CCD File 
I [auth C],
K [auth C]
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
1Y8
Query on 1Y8

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
J [auth C]
2-(trimethyl-lambda~5~-arsanyl)ethanol
C5 H14 As O
CIHXLIBMYUSRLN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.47α = 90
b = 129.69β = 90
c = 164.65γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2014-07-30
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations