5MB4

Crystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Literature

Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin.

Ribeiro, J.P., Ali Abol Hassan, M., Rouf, R., Tiralongo, E., May, T.W., Day, C.J., Imberty, A., Tiralongo, J., Varrot, A.

(2017) Proteins 85: 969-975

  • DOI: https://doi.org/10.1002/prot.25265
  • Primary Citation of Related Structures:  
    5MB4

  • PubMed Abstract: 

    A lectin with strong cytotoxic effect on human colon cancer HT29 and monkey kidney VERO cells was recently identified from the Australian indigenous mushroom Psathyrella asperospora and named PAL. We herein present its biochemical and structural analysis using a multidisciplinary approach. Glycan arrays revealed binding preference towards N-acetylglucosamine (GlcNAc) and, to a lesser extent, towards sialic acid (Neu5Ac). Submicromolar and millimolar affinity was measured by surface plasmon resonance for GlcNAc and NeuAc, respectively. The structure of PAL was resolved by X-ray crystallography, elucidating both the protein's amino acid sequence as well as the molecular basis rationalizing its binding specificity. Proteins 2017; 85:969-975. © 2016 Wiley Periodicals, Inc.

    • Organizational Affiliation: 

    CERMAV, UPR5301, CNRS and Université Grenoble Alpes, Grenoble, 38041, France.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlcNAc specific lectin401PsathyrellaMutation(s): 0 
UniProt
Find proteins for A0A1U7Q1Z0 (Psathyrella)
Explore A0A1U7Q1Z0 
Go to UniProtKB:  A0A1U7Q1Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U7Q1Z0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG
Download Ideal Coordinates CCD File 
J [auth A],
P [auth A]		2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
I [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MLI
Query on MLI
Download Ideal Coordinates CCD File 
H [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NDG Binding MOAD:  5MB4 Kd: 450 (nM) from 1 assay(s)
NAG Binding MOAD:  5MB4 Kd: 450 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.55α = 90
b = 120.55β = 90
c = 198.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Labex ArcaneFranceANR-11-LABX-0003-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary