5HCF

T. cruzi calreticulin globular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.

Moreau, C.Cioci, G.Iannello, M.Laffly, E.Chouquet, A.Ferreira, A.Thielens, N.M.Gaboriaud, C.

(2016) IUCrJ 3: 408-419

  • DOI: https://doi.org/10.1107/S2052252516012847
  • Primary Citation of Related Structures:  
    5HCA, 5HCB, 5HCF, 5LK5

  • PubMed Abstract: 

    Calreticulin (CRT) is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER) chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant 'eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi , Entamoeba histolytica , Taenia solium , Leishmania donovani and Schistosoma mansoni . Because of the inherent flexibility of CRTs, their analysis by X-ray crystallography requires the design of recombinant constructs suitable for crystallization, and thus only the structures of two very similar mammalian CRT lectin domains are known. With the X-ray structures of two distant parasite CRTs, insights into species structural determinants that might be harnessed to fight against the parasites without affecting the functions of the host CRT are now provided. Moreover, although the hypothesis that CRT can exhibit both open and closed conformations has been proposed in relation to its chaperone function, only the open conformation has so far been observed in crystal structures. The first evidence is now provided of a complex conformational transition with the junction reoriented towards P-domain closure. SAXS experiments also provided additional information about the flexibility of T. cruzi CRT in solution, thus complementing crystallographic data on the open conformation. Finally, regarding the conserved lectin-domain structure and chaperone function, evidence is provided of its dual carbohydrate/protein specificity and a new scheme is proposed to interpret such unusual substrate-binding properties. These fascinating features are fully consistent with previous experimental observations, as discussed considering the broad spectrum of CRT sequence conservations and differences.


  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calreticulin, putative,Calreticulin, putative
A, B, C, D, E
A, B, C, D, E, F
271Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053510685.10
UniProt
Find proteins for Q4CPZ0 (Trypanosoma cruzi (strain CL Brener))
Explore Q4CPZ0 
Go to UniProtKB:  Q4CPZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4CPZ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
J [auth B],
O [auth F]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth C],
M [auth E],
N [auth E]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.3α = 95.57
b = 79.38β = 98.69
c = 85.08γ = 119.86
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR 09-PIRI-0021

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2016-12-21
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary