2LMS | pdb_00002lms

A single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site

• PDB DOI: https://doi.org/10.2210/pdb2LMS/pdb
• BMRB: 18135

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-12 Released: 2012-12-05 
• Deposition Author(s): Ghasriani, H., Belcourt, P.J.F., Sauve, S., Hodgson, D.J., Gingras, G., Brochu, D., Gilbert, M., Aubin, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

A single N-acetylgalactosamine residue at threonine 106 modifies the dynamics and structure of interferon alpha2a around the glycosylation site.

Ghasriani, H., Belcourt, P.J., Sauve, S., Hodgson, D.J., Brochu, D., Gilbert, M., Aubin, Y.

(2013) J Biological Chem 288: 247-254

• PubMed: 23184955 
• DOI: https://doi.org/10.1074/jbc.M112.413252
• Primary Citation Related Structures: 
  2LMS


• PubMed Abstract: 
  

  Enzymatic addition of GalNAc to isotopically labeled IFNα2a produced in Escherichia coli yielded the O-linked glycoprotein GalNAcα-[(13)C,(15)N]IFNα2a. The three-dimensional structure of GalNAcα-IFNα2a has been determined in solution by NMR spectroscopy at high resolution. Proton-nitrogen heteronuclear Overhauser enhancement measurements revealed that the addition of a single monosaccharide unit at Thr-106 significantly slowed motions of the glycosylation loop on the nanosecond time scale. Subsequent addition of a Gal unit produced Gal(β1,3)GalNAcα-[(13)C,(15)N]IFNα2a. This extension resulted in a further decrease in the dynamics of this loop. The methodology used here allowed the first such description of the structure and dynamics of an O-glycoprotein and opens the way to the study of this class of proteins.

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Organizational Affiliation: 
• Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.62 kDa 
• Atom Count: 1,364 
• Modeled Residue Count: 165 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon alpha-2	A	166	Homo sapiens	Mutation(s): 0  Gene Names: IFNA2
UniProt & NIH Common Fund Data Resources
Find proteins for P01563 (Homo sapiens) Explore P01563  Go to UniProtKB:  P01563
PHAROS:  P01563 GTEx:  ENSG00000188379
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01563-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	B [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Ghasriani, H., Belcourt, P.J.F., Sauve, S., Hodgson, D.J., Gingras, G., Brochu, D., Gilbert, M., Aubin, Y.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-06-14
  Changes: Database references, Other, Structure summary
• Version 2.2: 2024-11-27
  Changes: Data collection, Database references, Structure summary