2VSD | pdb_00002vsd

crystal structure of CHIR-AB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.247 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 4.2 of the entry. See complete history

Literature

The Crystal Structure of Chir-Ab1: A Primordial Avian Classical Fc Receptor.

Arnon, T.I.Kaiser, J.T.West, A.P.Olson, R.Diskin, R.Viertlboeck, B.C.Gobel, T.W.Bjorkman, P.J.

(2008) J Mol Biology 381: 1012

  • DOI: https://doi.org/10.1016/j.jmb.2008.06.082
  • Primary Citation Related Structures: 
    2VSD

  • PubMed Abstract: 

    CHIR-AB1 is a newly identified avian immunoglobulin (Ig) receptor that includes both activating and inhibitory motifs and was therefore classified as a potentially bifunctional receptor. Recently, CHIR-AB1 was shown to bind the Fc region of chicken IgY and to induce calcium mobilization via association with the common gamma-chain, a subunit that transmits signals upon ligation of many different immunoreceptors. Here we describe the 1.8-A-resolution crystal structure of the CHIR-AB1 ectodomain. The receptor ectodomain consists of a single C2-type Ig domain resembling the Ig-like domains found in mammalian Fc receptors such as FcgammaRs and FcalphaRI. Unlike these receptors and other monomeric Ig superfamily members, CHIR-AB1 crystallized as a 2-fold symmetrical homodimer that bears no resemblance to variable or constant region dimers in an antibody. Analytical ultracentrifugation demonstrated that CHIR-AB1 exists as a mixture of monomers and dimers in solution, and equilibrium gel filtration revealed a 2:1 receptor/ligand binding stoichiometry. Measurement of the 1:1 CHIR-AB1/IgY interaction affinity indicates a relatively low affinity complex, but a 2:1 CHIR-AB1/IgY interaction allows an increase in apparent affinity due to avidity effects when the receptor is tethered to a surface. Taken together, these results add to the structural understanding of Fc receptors and their functional mechanisms.


  • Organizational Affiliation
    • Division of Biology, 114-96 and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 12.61 kDa 
  • Atom Count: 875 
  • Modeled Residue Count: 93 
  • Deposited Residue Count: 105 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHIR AB1105Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q5ZJ90 (Gallus gallus)
Explore Q5ZJ90 
Go to UniProtKB:  Q5ZJ90
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZJ90
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.247 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.695α = 90
b = 63.695β = 90
c = 55.453γ = 120
Software Package:
Software NamePurpose
PHASERphasing
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-09-11
    Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Structure summary
  • Version 3.0: 2019-10-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 4.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 4.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 4.2: 2024-11-20
    Changes: Structure summary