4WVW | pdb_00004wvw

Chicken Galectin-8 N-terminal domain complexed with 3'-sialyl-lactose

• PDB DOI: https://doi.org/10.2210/pdb4WVW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-07 Released: 2015-09-23 
• Deposition Author(s): Ruiz, F.M., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes.

Ruiz, F.M., Gilles, U., Lindner, I., Andre, S., Romero, A., Reusch, D., Gabius, H.J.

(2015) Chemistry 21: 13558-13568

• PubMed: 26270612 
• DOI: https://doi.org/10.1002/chem.201501961
• Primary Citation Related Structures: 
  4WVV, 4WVW


• PubMed Abstract: 
  

  The physiological significance arising from translating information stored in glycans into cellular effects explains the interest in structurally defining lectin-carbohydrate recognition. The relatively small set of adhesion/growth-regulatory galectins in chicken makes this system attractive to study the origins of specificity and divergence. Cell binding by using glycosylation mutants reveals binding of the N-terminal domain of chicken galectin-8 (CG-8N) to α-2,3-sialylated and galactose-terminated glycan chains. Cocrystals with lactose and its 3'-sialylated derivative disclose Arg58 as a key contact for the carboxylic acid and differences in loop lengths to the three homodimeric chicken galectins. Monitoring hydrogen-deuterium exchange by mass spectrometry revealed an effective reduction of deuteration after ligand binding within the contact area. In addition, evidence for changes in solvent accessibility of amide protons beyond this site was obtained. Their detection, which highlights the sensor capacity of this technique, encourages systematic studies on galectins and beyond.

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Organizational Affiliation: 
• Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9 28040 Madrid (Spain).
Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg (Germany).
Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstrasse 13, 80539 München (Germany). [e-mail].
Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9 28040 Madrid (Spain). [e-mail].
Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg (Germany). [e-mail].
Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstrasse 13, 80539 München (Germany).

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: 17.26 kDa 
• Atom Count: 1,428 
• Modeled Residue Count: 144 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin	A	144	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for Q1W2P6 (Gallus gallus) Explore Q1W2P6  Go to UniProtKB:  Q1W2P6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G92323ZH GlyCosmos: G92323ZH GlyGen: G92323ZH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900025	B	3'-sialyl-alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.459	α = 90
b = 56.459	β = 90
c = 198.987	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Ruiz, F.M., Romero, A.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary