5WXU

11S globulin from Wrightia tinctoria reveals auxin binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin.

Kumar, P.Kesari, P.Dhindwal, S.Choudhary, A.K.Katiki, M.Verma, A.Ambatipudi, K.Tomar, S.Sharma, A.K.Mishra, G.Kumar, P.

(2017) Sci Rep 7: 4705-4705

  • DOI: https://doi.org/10.1038/s41598-017-04518-7
  • Primary Citation of Related Structures:  
    5WXU

  • PubMed Abstract: 

    Auxin levels are tightly regulated within the plant cell, and its storage in the isolated cavity of proteins is a measure adopted by cells to maintain the availability of auxin. We report the first crystal structure of Wrightia tinctoria 11S globulin (WTG) in complex with Indole-3-acetic acid (IAA), an auxin, at 1.7 Å resolution. WTG hexamers assemble as a result of the stacking interaction between the hydrophobic surfaces of two trimers, leaving space for the binding of charged ligands. The bound auxin is stabilized by non-covalent interactions, contributed by four chains in each cavity. The presence of bound ligand was confirmed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and high-resolution mass spectrometry (HRMS). Here, we hypothesize that the cleavage of globulins by endopeptidases leads to the movement of the hydrophilic loop region from the surface to the periphery, leaving space for the binding of auxin, and promotes hexamer formation. As the process of germination proceeds, there is a change in the pH, which induces the dissociation of the hexamer and the release of auxin. The compact hexameric assembly ensures the long-term, stable storage of the hormone. This suggests a role for globulin as a novel player in auxin homeostasis.


  • Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
11S globulin
A, B, C, D, E
A, B, C, D, E, F
479Wrightia tinctoriaMutation(s): 0 
UniProt
Find proteins for A0A162EGL7 (Wrightia tinctoria)
Explore A0A162EGL7 
Go to UniProtKB:  A0A162EGL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A162EGL7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
BA [auth D]
I [auth A]
JA [auth E]
NA [auth F]
Q [auth B]
BA [auth D],
I [auth A],
JA [auth E],
NA [auth F],
Q [auth B],
U [auth C]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
IAC
Query on IAC

Download Ideal Coordinates CCD File 
FA [auth D],
M [auth A],
S [auth B]
1H-INDOL-3-YLACETIC ACID
C10 H9 N O2
SEOVTRFCIGRIMH-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth D],
LA [auth E],
RA [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth D]
DA [auth D]
G [auth A]
GA [auth E]
AA [auth D],
CA [auth D],
DA [auth D],
G [auth A],
GA [auth E],
H [auth A],
HA [auth E],
KA [auth E],
MA [auth E],
N [auth B],
O [auth B],
OA [auth F],
PA [auth F],
QA [auth F],
R [auth B],
X [auth C],
Y [auth C],
Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
IA [auth E]
J [auth A]
K [auth A]
L [auth A]
P [auth B]
IA [auth E],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
SA [auth F],
T [auth B],
V [auth C],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.209α = 90
b = 114.242β = 90
c = 202.479γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary