5AV7

Crystal structure of Calsepa lectin in complex with bisected glycan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins

Nagae, M.Kanagawa, M.Morita-Matsumoto, K.Hanashima, S.Kizuka, Y.Taniguchi, N.Yamaguchi, Y.

(2016) Sci Rep 6: 22973-22973

  • DOI: 10.1038/srep22973
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylgluco ...

    Glycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylglucosamine (GlcNAc), is potentially a good model for investigating conformational dynamics and glycan-lectin interactions, owing to the unique ability of this sugar residue to alter conformer populations and thus modulate the biological activities. Here we analyzed bisected glycan in complex with two unrelated lectins, Calsepa and PHA-E. The crystal structures of the two complexes show a conspicuous flipped back glycan structure (designated 'back-fold' conformation), and solution NMR analysis also provides evidence of 'back-fold' glycan structure. Indeed, statistical conformational analysis of available bisected and non-bisected glycan structures suggests that bisecting GlcNAc restricts the conformations of branched structures. Restriction of glycan flexibility by certain sugar residues may be more common than previously thought and impinges on the mechanism of glycoform-dependent biological functions.


    Organizational Affiliation

    Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lectin
A, B, C, D
151Calystegia sepiumMutation(s): 0 
Find proteins for P93114 (Calystegia sepium)
Go to UniProtKB:  P93114
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MMA
Query on MMA

Download SDF File 
Download CCD File 
A, C
O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 47.608α = 90.01
b = 52.836β = 90.03
c = 54.774γ = 94.05
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan15K18496, 26110724

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release