6H7D | pdb_00006h7d

Crystal Structure of A. thaliana Sugar Transport Protein 10 in complex with glucose in the outward occluded state

• PDB DOI: https://doi.org/10.2210/pdb6H7D/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-07-31 Released: 2019-02-06 
• Deposition Author(s): Pedersen, B.P., Paulsen, P.A., Custodio, T.F.
• Funding Organization(s): Danish Council for Independent Research, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily.

Paulsen, P.A., Custodio, T.F., Pedersen, B.P.

(2019) Nat Commun 10: 407-407

• PubMed: 30679446 
• DOI: https://doi.org/10.1038/s41467-018-08176-9
• Primary Citation Related Structures: 
  6H7D


• PubMed Abstract: 
  

  Plants are dependent on controlled sugar uptake for correct organ development and sugar storage, and apoplastic sugar depletion is a defense strategy against microbial infections like rust and mildew. Uptake of glucose and other monosaccharides is mediated by Sugar Transport Proteins, proton-coupled symporters from the Monosaccharide Transporter (MST) superfamily. We present the 2.4 Å structure of Arabidopsis thaliana high affinity sugar transport protein, STP10, with glucose bound. The structure explains high affinity sugar recognition and suggests a proton donor/acceptor pair that links sugar transport to proton translocation. It contains a Lid domain, conserved in all STPs, that locks the mobile transmembrane domains through a disulfide bridge, and creates a protected environment which allows efficient coupling of the proton gradient to drive sugar uptake. The STP10 structure illuminates fundamental principles of sugar transport in the MST superfamily with implications for both plant antimicrobial defense, organ development and sugar storage.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark. [e-mail].
Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000, Aarhus C, Denmark. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 59.32 kDa 
• Atom Count: 3,969 
• Modeled Residue Count: 487 
• Deposited Residue Count: 521 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar transport protein 10	A	521	Arabidopsis thaliana	Mutation(s): 0  Gene Names: STP10, At3g19940, MPN9.19 Membrane Entity: Yes
UniProt
Find proteins for Q9LT15 (Arabidopsis thaliana) Explore Q9LT15  Go to UniProtKB:  Q9LT15

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
P33	C [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
BGC (Subject of Investigation/LOI)	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.68	α = 90
b = 92.46	β = 109.37
c = 66.8	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Pedersen, B.P., Paulsen, P.A., Custodio, T.F.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	DFF-4002-0052
European Research Council	Denmark	StG-637372

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Data collection
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary