6LEO | pdb_00006leo

Crystal structure of thiosulfate transporter YeeE from Spirochaeta thermophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.252 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake.

Tanaka, Y.Yoshikaie, K.Takeuchi, A.Ichikawa, M.Mori, T.Uchino, S.Sugano, Y.Hakoshima, T.Takagi, H.Nonaka, G.Tsukazaki, T.

(2020) Sci Adv 6: eaba7637-eaba7637

  • DOI: https://doi.org/10.1126/sciadv.aba7637
  • Primary Citation Related Structures: 
    6LEO, 6LEP

  • PubMed Abstract: 

    We have demonstrated that a bacterial membrane protein, YeeE, mediates thiosulfate uptake. Thiosulfate is used for cysteine synthesis in bacteria as an inorganic sulfur source in the global biological sulfur cycle. The crystal structure of YeeE at 2.5-Å resolution reveals an unprecedented hourglass-like architecture with thiosulfate in the positively charged outer concave side. YeeE is composed of loops and 13 helices including 9 transmembrane α helices, most of which show an intramolecular pseudo 222 symmetry. Four characteristic loops are buried toward the center of YeeE and form its central region surrounded by the nine helices. Additional electron density maps and successive molecular dynamics simulations imply that thiosulfate can remain temporally at several positions in the proposed pathway. We propose a plausible mechanism of thiosulfate uptake via three important conserved cysteine residues of the loops along the pathway.


  • Organizational Affiliation
    • Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.

Macromolecule Content 

  • Total Structure Weight: 39.72 kDa 
  • Atom Count: 2,784 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 339 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulf_transp domain-containing protein339Winmispira thermophilaMutation(s): 0 
Gene Names: Spith_0734
Membrane Entity: Yes 
UniProt
Find proteins for G0GAP6 (Winmispira thermophila (strain ATCC 700085 / DSM 6578 / Z-1203))
Explore G0GAP6 
Go to UniProtKB:  G0GAP6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0GAP6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
THJ
(Subject of Investigation/LOI)

Query on THJ



Download:Ideal Coordinates CCD File
B [auth A]THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.252 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.51α = 90
b = 95.32β = 90
c = 101.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP19K06526, JP19K22395, JP19H05639

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary