6FOF

Crystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/VII-IX]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Crystallization of a human galectin-3 variant with two ordered segments in the shortened N-terminal tail.

Flores-Ibarra, A., Vertesy, S., Medrano, F.J., Gabius, H.J., Romero, A.

(2018) Sci Rep 8: 9835-9835

  • DOI: https://doi.org/10.1038/s41598-018-28235-x
  • Primary Citation of Related Structures:  
    6FOF

  • PubMed Abstract: 

    Among members of the family of adhesion/growth-regulatory galectins, galectin-3 (Gal-3) bears a unique modular architecture. A N-terminal tail (NT) consisting of the N-terminal segment (NTS) and nine collagen-like repeats is linked to the canonical lectin domain. In contrast to bivalent proto- and tandem-repeat-type galectins, Gal-3 is monomeric in solution, capable to self-associate in the presence of bi- to multivalent ligands, and the NTS is involved in cellular compartmentalization. Since no crystallographic information on Gal-3 beyond the lectin domain is available, we used a shortened variant with NTS and repeats VII-IX. This protein crystallized as tetramers with contacts between the lectin domains. The region from Tyr101 (in repeat IX) to Leu114 (in the CRD) formed a hairpin. The NTS extends the canonical β-sheet of F1-F5 strands with two new β-strands on the F face. Together, crystallographic and SAXS data reveal a mode of intramolecular structure building involving the highly flexible Gal-3's NT.

    • Organizational Affiliation: 

    Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3,Galectin-3196Homo sapiensMutation(s): 0 
Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
PHAROS:  P17931
GTEx:  ENSG00000131981 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17931
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth D]
DA [auth D]
EA [auth E]
AA [auth C],
BA [auth C],
CA [auth D],
DA [auth D],
EA [auth E],
FA [auth G],
GA [auth G],
HA [auth G],
IA [auth B],
JA [auth B],
KA [auth F],
LA [auth H],
MA [auth H],
NA [auth H],
OA [auth H],
PA [auth I],
QA [auth I],
RA [auth J],
SA [auth K],
TA [auth K],
UA [auth K],
VA [auth L],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.851α = 90
b = 98.195β = 90
c = 237.814γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBFU2016-77835-R

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary