5GVY image
Deposition Date 2016-09-07
Release Date 2017-09-13
Last Version Date 2023-11-08
Entry Detail
PDB ID:
5GVY
Title:
Crystal structure of SALT protein from Oryza sativa
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.66 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Salt stress-induced protein
Gene (Uniprot):SALT
Chain IDs:A, B
Chain Length:145
Number of Molecules:2
Biological Source:Oryza sativa subsp. indica
Ligand Molecules
Primary Citation
Structural insights into rice SalTol QTL located SALT protein.
Sci Rep 10 16589 16589 (2020)
PMID: 33024209 DOI: 10.1038/s41598-020-73517-y

Abstact

Salinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 Å). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 Å2 compared to only 240 Å2 for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.

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Primary Citation of related structures