6D9Z | pdb_00006d9z

Structure of CysZ, a sulfate permease from Pseudomonas Denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.289 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BOGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structure-based analysis of CysZ-mediated cellular uptake of sulfate.

Assur Sanghai, Z.Liu, Q.Clarke, O.B.Belcher-Dufrisne, M.Wiriyasermkul, P.Giese, M.H.Leal-Pinto, E.Kloss, B.Tabuso, S.Love, J.Punta, M.Banerjee, S.Rajashankar, K.R.Rost, B.Logothetis, D.Quick, M.Hendrickson, W.A.Mancia, F.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.27829
  • Primary Citation of Related Structures:  
    6D79, 6D9Z

  • PubMed Abstract: 

    Sulfur, most abundantly found in the environment as sulfate (SO 4 2- ), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO 4 2- at the molecular level is limited. CysZ has been described as a SO 4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO 4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO 4 2- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues.


  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University, New York, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfate transporter CysZ246Pseudomonas denitrificans (nom. rej.)Mutation(s): 0 
Gene Names: cysZ
Membrane Entity: Yes 
UniProt
Find proteins for M4XKU7 (Pseudomonas sp. ATCC 13867)
Explore M4XKU7 
Go to UniProtKB:  M4XKU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4XKU7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
G [auth F]
H [auth F]
I [auth F]
J [auth F]
K [auth F]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.289 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.13α = 90
b = 225.13β = 90
c = 96.62γ = 120
Software Package:
Software NamePurpose
phenix.refinerefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BOGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098617
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107462
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM095315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM116799

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary