2W59 | pdb_00002w59

STRUCTURE OF AN AVIAN IGY-FC 3-4 FRAGMENT

• PDB DOI: https://doi.org/10.2210/pdb2W59/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2008-12-08 Released: 2009-01-13 
• Deposition Author(s): Fabiane, S.M., Taylor, A.I., Sutton, B.J., Calvert, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.196 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of an Avian Igy-Fc Fragment Reveals Conservation with Both Mammalian Igg and Ige.

Taylor, A.I., Fabiane, S.M., Sutton, B.J., Calvert, R.A.

(2009) Biochemistry 48: 558

• PubMed: 19115948 
• DOI: https://doi.org/10.1021/bi8019993
• Primary Citation Related Structures: 
  2W59


• PubMed Abstract: 
  

  Avian IgY is closely related to an ancestor of both mammalian IgG and IgE and thus provides insights into the evolution of antibody structure and function. A recombinant fragment of IgY-Fc consisting of a dimer of the Cupsilon3 and Cupsilon4 domains, Fcupsilon3-4, was expressed and crystallized and its X-ray structure determined to 1.75 A resolution. Fcupsilon3-4 is the only nonmammalian Fc fragment structure determined to date and provides the first structural evidence for an ancient origin of antibody architecture. The Fcupsilon3-4 structure reveals features common to both IgE-Fc and IgG-Fc, and the implications for IgY binding to its receptor are discussed.

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Organizational Affiliation: 
• Randall Division of Cell and Molecular Biophysics, King's College London, and MRC-Asthma UK Centre in Allergic Mechanisms of Asthma, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 52.71 kDa 
• Atom Count: 4,072 
• Modeled Residue Count: 429 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGY FCU3-4	A, B	231	Gallus gallus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.196 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.481	α = 90
b = 80.14	β = 90
c = 99.135	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Fabiane, S.M., Taylor, A.I., Sutton, B.J., Calvert, R.A.

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Advisory
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary