8BHD

N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes.

Jaramillo Ponce, J.R., Theobald-Dietrich, A., Benas, P., Paulus, C., Sauter, C., Frugier, M.

(2023) Protein Sci : e4564-e4564

  • DOI: 10.1002/pro.4564
  • Primary Citation of Related Structures:  
    8BCQ, 8BHD

  • PubMed Abstract: 

    • tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases ...

    tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases. In eukaryotes, such multi-aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N-terminal GST-like domain involved in the assembly of two independent complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST-like domains of tRip and ERS (tRip-N:ERS-N) is central. In this study, the crystal structure of the N-terminal GST-like domain of ERS was solved and made possible further investigation of the solution architecture of the Q- and M-complexes by small-angle X-ray scattering (SAXS). This strategy relied on the engineering of a tRip-N-ERS-N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed. This article is protected by copyright. All rights reserved.

    Related Citations: 
    • Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein.
      Jaramillo Ponce, J.R., Kapps, D., Paulus, C., Chicher, J., Frugier, M.
      (2022) J Biol Chem 298: 101987
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
      Liebschner, D., Afonine, P.V., Baker, M.L., Bunkoczi, G., Chen, V.B., Croll, T.I., Hintze, B., Hung, L.W., Jain, S., McCoy, A.J., Moriarty, N.W., Oeffner, R.D., Poon, B.K., Prisant, M.G., Read, R.J., Richardson, J.S., Richardson, D.C., Sammito, M.D., Sobolev, O.V., Stockwell, D.H., Terwilliger, T.C., Urzhumtsev, A.G., Videau, L.L., Williams, C.J., Adams, P.D.
      (2019) Acta Crystallogr D Struct Biol 75: 861
    • Coot: model-building tools for molecular graphics.
      Emsley, P., Cowtan, K.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 2126
    • The Buccaneer software for automated model building. 1. Tracing protein chains.
      Cowtan, K.
      (2006) Acta Crystallogr D Biol Crystallogr 62: 1002
    • Recent developments in classical density modification.
      Cowtan, K.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 470
    • Multivariate phase combination improves automated crystallographic model building.
      Skubak, P., Waterreus, W.J., Pannu, N.S.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 783
    • Methods used in the structure determination of bovine mitochondrial F1 ATPase.
      Abrahams, J.P., Leslie, A.G.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 30
    • REFMAC5 for the refinement of macromolecular crystal structures.
      Murshudov, G.N., Skubak, P., Lebedev, A.A., Pannu, N.S., Steiner, R.A., Nicholls, R.A., Winn, M.D., Long, F., Vagin, A.A.
      (2011) Acta Crystallogr D Biol Crystallogr 67: 355
    • Substructure solution with SHELXD.
      Schneider, T.R., Sheldrick, G.M.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1772
    • A short history of SHELX.
      Sheldrick, G.M.
      (2008) Acta Crystallogr A 64: 112
    • Automatic protein structure solution from weak X-ray data.
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      (2013) Nat Commun 4: 2777
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      Kabsch, W.
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      (2019) J Synchrotron Radiat 26: 393
    • Status of the crystallography beamlines at synchrotron SOLEIL⋆
      Coati, A., Chavas, L.M.G., Fontaine, P., Foos, N., Guimaraes, B., Gourhant, P., Legrand, P., Itie, J.P., Fertey, P., Shepard, W., Isabet, T., Sirigu, S., Solari, P.L., Thiaudiere, D., Thompson, A.
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    • Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
      Engilberge, S., Riobe, F., Di Pietro, S., Lassalle, L., Coquelle, N., Arnaud, C.A., Pitrat, D., Mulatier, J.C., Madern, D., Breyton, C., Maury, O., Girard, E.
      (2017) Chem Sci 8: 5909
    Organizational Affiliation: 

    Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate--tRNA ligaseA, B, C, D, E249Plasmodium berghei ANKAMutation(s): 0 
Gene Names: PBANKA_1362000
EC: 6.1.1.17
UniProt
Find proteins for A0A509AR09 (Plasmodium berghei (strain Anka))
Explore A0A509AR09 
Go to UniProtKB:  A0A509AR09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A509AR09
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth C],
BA [auth C],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth E],
HA [auth E],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
T [auth B],
U [auth B],
V [auth B],
Y [auth C],
Z [auth C]
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
Q [auth B],
R [auth B],
W [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
S [auth B],
X [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.11α = 90
b = 88.51β = 105.7
c = 168.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CRANK2phasing
XSCALEdata scaling
XDSdata reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-IDEX-0002
Agence Nationale de la Recherche (ANR)FranceANR 20-SFRI-0012
Agence Nationale de la Recherche (ANR)FranceANR-17-EURE-0023

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release