5XPD | pdb_00005xpd

Sugar transporter of AtSWEET13 in inward-facing state with a substrate analog

• PDB DOI: https://doi.org/10.2210/pdb5XPD/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2017-06-01 Released: 2017-09-13 
• Deposition Author(s): Han, L., Zhang, X.J.
• Funding Organization(s): the Ministry of Science and Technology, the Chinese Academy of Sciences, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Models: experimental

Literature

Molecular mechanism of substrate recognition and transport by the AtSWEET13 sugar transporter

Han, L., Zhu, Y.P., Liu, M., Zhou, Y., Lu, G.Y., Lan, L., Wang, X.P., Zhao, Y.F., Zhang, X.C.

(2017) Proc Natl Acad Sci U S A 114: 10089-10094

• PubMed: 28878024 
• DOI: https://doi.org/10.1073/pnas.1709241114
• Primary Citation Related Structures: 
  5XPD


• PubMed Abstract: 
  

  Sugar Will Eventually be Exported Transporters (SWEETs) are recently identified sugar transporters that can discriminate and transport di- or monosaccharides across a membrane following the concentration gradient. SWEETs play key roles in plant biological processes, such as pollen nutrition, nectar secretion, seed filling, and phloem loading. SWEET13 from Arabidopsis thaliana (AtSWEET13) is an important sucrose transporter in pollen development. Here, we report the 2.8-Å resolution crystal structure of AtSWEET13 in the inward-facing conformation with a substrate analog, 2'-deoxycytidine 5'-monophosphate, bound in the central cavity. In addition, based on the results of an in-cell transport activity assay and single-molecule Förster resonance energy transfer analysis, we suggest a mechanism for substrate selectivity based on the size of the substrate-binding pocket. Furthermore, AtSWEET13 appears to form a higher order structure presumably related to its function.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.31 kDa 
• Atom Count: 2,124 
• Modeled Residue Count: 269 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar transporter	A	293	Arabidopsis thaliana	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9FGQ2 (Arabidopsis thaliana) Explore Q9FGQ2  Go to UniProtKB:  Q9FGQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCM	B [auth A]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.78	α = 90
b = 42.831	β = 93.85
c = 116.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Han, L., Zhang, X.J.

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Funding Organization	Location	Grant Number
the Ministry of Science and Technology	China	2014CB910104 to XCZ
the Chinese Academy of Sciences	China	XDB080203 to XCZ
National Natural Science Foundation of China	China	31470745 to XCZ

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description