Crystal structure of SemiSWEET in the inward-open conformation

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history


Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

Lee, Y.Nishizawa, T.Yamashita, K.Ishitani, R.Nureki, O.

(2015) Nat Commun 6: 6112-6112

  • DOI: https://doi.org/10.1038/ncomms7112
  • Primary Citation of Related Structures:  
    4X5M, 4X5N

  • PubMed Abstract: 

    SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the 'binder clip-like' motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C
100Escherichia coli UMEA 3162-1Mutation(s): 0 
Gene Names: G925_04926
Membrane Entity: Yes 
Find proteins for P0DMV3 (Escherichia coli (strain UMEA 3162-1))
Explore P0DMV3 
Go to UniProtKB:  P0DMV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DMV3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on OLB

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G [auth A],
R [auth B]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on OLA

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D [auth A]
E [auth A]
F [auth A]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
T [auth C]
C18 H34 O2
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B],
S [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.68α = 90
b = 102.12β = 90
c = 58.95γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations, Source and taxonomy