4X5M

Crystal structure of SemiSWEET in the inward-open conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

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: 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) ...

    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: 

    Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B, C100Escherichia coli UMEA 3162-1Mutation(s): 0 
Gene Names: G925_04926
Membrane Entity: Yes 
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
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
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
OLB
Query on OLB
Download Ideal Coordinates CCD File 
G [auth A],
R [auth B]		(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N		 Ligand Interaction
OLA
Query on OLA
Download Ideal Coordinates CCD File 
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]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth B],
S [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement

Structure Validation

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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