4BPQ | pdb_00004bpq

Structure and substrate induced conformational changes of the secondary citrate-sodium symporter CitS revealed by electron crystallography


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.00 Å

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure and Substrate-Induced Conformational Changes of the Secondary Citrate/Sodium Symporter Cits Revealed by Electron Crystallography.

Kebbel, F.Kurz, M.Arheit, M.Grutter, M.G.Stahlberg, H.

(2013) Structure 21: 1243

  • DOI: https://doi.org/10.1016/j.str.2013.05.011
  • Primary Citation Related Structures: 
    4BPQ

  • PubMed Abstract: 

    The secondary Na+/citrate symporter CitS of Klebsiella pneumoniae is the best-characterized member of the 2-hydroxycarboxylate transporter family. The recent projection structure gave insight into its overall structural organization. Here, we present the three-dimensional map of dimeric CitS obtained with electron crystallography. Each monomer has 13 a-helical transmembrane segments; six are organized in a distal helix cluster and seven in the central dimer interface domain. Based on structural analyses and comparison to VcINDY, we propose a molecular model for CitS, assign the helices, and demonstrate the internal structural symmetry. We also present projections of CitS in several conformational states induced by the presence and absence of sodium and citrate as substrates. Citrate binding induces a defined movement of a helices within the distal helical cluster. Based on this, we propose a substrate translocation site and conformational changes that are in agreement with the transport model of ‘‘alternating access’’.


  • Organizational Affiliation
    • Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 54.16 kDa 
  • Atom Count: 3,110 
  • Modeled Residue Count: 622 
  • Deposited Residue Count: 636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CITRATE\:SODIUM SYMPORTER
A, B
318Klebsiella pneumoniaeMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.00 Å
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 1α = 90
b = 1β = 90
c = 1γ = 90
Software Package:
Software NamePurpose
2DXmodel building
2DXrefinement
2DXdata scaling
2DXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Author supporting evidence, Data collection, Database references