5DA0

Structure of the the SLC26 transporter SLC26Dg in complex with a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family.

Geertsma, E.R.Chang, Y.N.Shaik, F.R.Neldner, Y.Pardon, E.Steyaert, J.Dutzler, R.

(2015) Nat Struct Mol Biol 22: 803-808

  • DOI: 10.1038/nsmb.3091
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The SLC26 family of membrane proteins combines a variety of functions within a conserved molecular scaffold. Its members, besides coupled anion transporters and channels, include the motor protein Prestin, which confers electromotility to cochlear ou ...

    The SLC26 family of membrane proteins combines a variety of functions within a conserved molecular scaffold. Its members, besides coupled anion transporters and channels, include the motor protein Prestin, which confers electromotility to cochlear outer hair cells. To gain insight into the architecture of this protein family, we characterized the structure and function of SLC26Dg, a facilitator of proton-coupled fumarate symport, from the bacterium Deinococcus geothermalis. Its modular structure combines a transmembrane unit and a cytoplasmic STAS domain. The membrane-inserted domain consists of two intertwined inverted repeats of seven transmembrane segments each and resembles the fold of the unrelated transporter UraA. It shows an inward-facing, ligand-free conformation with a potential substrate-binding site at the interface between two helix termini at the center of the membrane. This structure defines the common framework for the diverse functional behavior of the SLC26 family.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulphate transporterA505Deinococcus geothermalis DSM 11300Mutation(s): 0 
Gene Names: Dgeo_2773
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
SLC26 proton-coupled fumarate symporter in complex with nanobodies
Find proteins for Q1J2S8 (Deinococcus geothermalis (strain DSM 11300))
Explore Q1J2S8 
Go to UniProtKB:  Q1J2S8
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NanobodyB124Lama glamaMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download CCD File 
A
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.65α = 90
b = 117.28β = 100.09
c = 84.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
DMphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
SNSFSwitzerlandNCCR Structural Biology

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Database references