5MB4 | pdb_00005mb4

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

• PDB DOI: https://doi.org/10.2210/pdb5MB4/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Psathyrella
• Mutation(s): No 


• Deposited: 2016-11-07 Released: 2017-02-22 
• Deposition Author(s): Ribeiro, J., Varrot, A.
• Funding Organization(s): Labex Arcane

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

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

• PubMed: 28168856 
• DOI: https://doi.org/10.1002/prot.25265
• Primary Citation 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.

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Organizational Affiliation: 
• CERMAV, UPR5301, CNRS and Université Grenoble Alpes, Grenoble, 38041, France.
DCM, UMR5250, CNRS and Université Grenoble Alpes, Grenoble, 38041, France.
Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia.
School of Pharmacy and Griffith Health Institute, Griffith University, Gold Coast Campus, Queensland 4222, Australia.
Royal Botanic Gardens Victoria, Melbourne, Victoria, 3004, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.72 kDa 
• Atom Count: 3,515 
• Modeled Residue Count: 401 
• Deposited Residue Count: 401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GlcNAc specific lectin	A	401	Psathyrella	Mutation(s): 0
UniProt
Find proteins for A0A1U7Q1Z0 (Psathyrella) Explore A0A1U7Q1Z0  Go to UniProtKB:  A0A1U7Q1Z0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	J [auth A], P [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	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	H [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.55	α = 90
b = 120.55	β = 90
c = 198.95	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Ribeiro, J., Varrot, A.

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Funding Organization	Location	Grant Number
Labex Arcane	France	ANR-11-LABX-0003-01

Revision History  

• 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