8QPX | pdb_00008qpx

Crystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.250 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Unusual traits shape the architecture of the Ig ancestor molecule.

Urdiciain, A.Madej, T.Wang, J.Song, J.Erausquin, E.Youkharibache, P.Lopez-Sagaseta, J.

(2025) Commun Biol 8: 463-463

  • DOI: https://doi.org/10.1038/s42003-025-07830-5
  • Primary Citation of Related Structures:  
    8OVQ, 8QPX

  • PubMed Abstract: 

    Understanding the ancestral Ig domain's molecular structure and tracing the evolution of Ig-like proteins are fundamental components missing from our comprehension of their evolutionary trajectory and function. We have determined high-resolution structures of two Ig-like proteins from the evolutionary most ancestral phylum, Porifera. The structures reveal N-terminal Ig-like domains with an unconventional configuration of features that set them apart from canonical Ig domains. These findings prompted us to call this novel domain as Ig "Early Variable" (EV)-set. Remarkably, the EV-sets are linked to C1-set domains. To the best of our knowledge, the C1-set has not been previously reported in non-vertebrates. The IgV and IgC1 tandems and their combination into functional Ig-like receptors are part of the adaptive immune system in higher vertebrates, which allows for highly specific immune responses. By unveiling important clues into the molecular configuration of ancestral Ig domains, these findings challenge and expand our understanding of how immunity has evolved within its current landscape.


  • Organizational Affiliation
    • Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, 31008, Navarra, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine kinase (Fragment)232Geodia cydoniumMutation(s): 0 
Gene Names: TK_2L
UniProt
Find proteins for O18431 (Geodia cydonium)
Explore O18431 
Go to UniProtKB:  O18431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18431
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
B
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.250 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.91α = 90
b = 32.73β = 90.82
c = 92.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainMargarita Salas
Spanish Ministry of Science, Innovation, and UniversitiesSpainRYC-2017-21683

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-04-02
    Changes: Database references