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), 0.316 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6D9Z

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 172.25 kDa 
  • Atom Count: 11,815 
  • Modeled Residue Count: 1,433 
  • Deposited Residue Count: 1,476 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfate transporter CysZ246Pseudomonas denitrificans (nom. rej.)Mutation(s): 0 
Gene Names: cysZ

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]
G [auth F],
H [auth F],
I [auth F],
J [auth F],
K [auth F],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth E],
Z [auth E]
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), 0.316 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.270 (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 


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