2GM3

Crystal Structure of an Universal Stress Protein Family Protein from Arabidopsis Thaliana At3g01520 with AMP Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.461 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP.

Kim, D.O.J.Bitto, E.Bingman, C.A.Kim, H.J.Han, B.W.Phillips, G.N.

(2015) Proteins 83: 1368-1373

  • DOI: 10.1002/prot.24821

  • PubMed Abstract: 
  • Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contain ...

    Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain-containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N-terminal portion of a multi-domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP-like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann-like α/β overall fold. The bound AMP and conservation of residues in the ATP-binding loop suggest that the protein At3g01520 also belongs to the ATP-binding USP subfamily members.


    Organizational Affiliation

    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin, 53706.,Laboratory of Stem Cell and Molecular Pharmacology, College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea.,Department of Chemistry and Biochemistry, Georgian Court University, Lakewood, New Jersey, 08701.,BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas, 77251.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
unknown protein
A, B, C, D, E, F
175Arabidopsis thalianaMutation(s): 0 
Find proteins for Q8LGG8 (Arabidopsis thaliana)
Go to UniProtKB:  Q8LGG8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.461 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 63.351α = 75.45
b = 65.662β = 75.04
c = 73.014γ = 66.11
Software Package:
Software NamePurpose
RESOLVEphasing
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2016-06-08
    Type: Database references
  • Version 1.4: 2017-10-18
    Type: Refinement description