9DMX | pdb_00009dmx

Crystal structure of shark UrIg2 V-C1-C2-C3 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.275 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Models: experimental
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Literature

Origin of immunoglobulins and T cell receptors: A candidate gene for invasion by the RAG transposon.

Flajnik, M.F.Stanfield, R.L.Verissimo, A.Neely, H.R.Munoz-Merida, A.Criscitiello, M.F.Wilson, I.A.Ohta, Y.

(2025) Sci Adv 11: eadw1273-eadw1273

  • DOI: https://doi.org/10.1126/sciadv.adw1273
  • Primary Citation of Related Structures:  
    9DMX

  • PubMed Abstract: 

    Rearranging antigen receptors (AgRs) arose when a variable (V) domain exon was invaded by the recombination-activating gene (RAG) transposon ~500 million years ago. We show here that the elasmobranch immunoglobulin heavy (IgH) isotypes-IgM, IgW, and IgNAR-are linked near the αδ T cell receptor (TCRαδ) locus. This linkage presages the emergence of the osteichthyan IgH translocon arrangement and clarifies the relationship between IgH and TCRδs. Recently, we reported UrIg , a nonrearranging, elasmobranch major histocompatibility complex (MHC)-linked AgR gene. Here, we describe a nonrearranging UrIg paralogue, UrIg2 , linked to this IgM/IgNAR/IgW/TCRαδ gene cluster in an AgR complex (AgRC). UrIg2 amino-terminal domains make homodimers where the C2-C3 structure resembles IgGFc. A relative of the UrIg2 V domain exon was invaded by the RAG transposon, revealing the genesis of the adaptive immune system. Our data indicate that an ancestral chromosome encoded an AgR precursor, undergoing RAG-mediated rearrangement after genome-wide duplication on one chromosome and retaining nonrearranging relics in the MHC and AgRC.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UrIg2 V-C1-C2-C3
A, B
457Ginglymostoma cirratumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.275 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.952α = 90
b = 97.384β = 90
c = 176.779γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release