9QG8 | pdb_00009qg8

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

MHC I of the Great Reed Warbler Promotes a Flat Peptide Binding Mode.

Venskutonyte, R.Kjellstrom, S.O'Connor, E.A.Westerdahl, H.Lindkvist-Petersson, K.

(2025) Immunology 176: 508-519

  • DOI: https://doi.org/10.1111/imm.70015
  • Primary Citation Related Structures: 
    9QG8

  • PubMed Abstract: 

    The major histocompatibility complex (MHC) plays a key role in pathogen recognition as part of the adaptive immune system. MHC I gene copy numbers in birds of the order Passeriformes (songbirds) are substantially larger compared to other birds. MHC I diversity and antigen presentation have been carefully characterised in chicken Gallus gallus of the order Galliformes; chickens express few MHC I genes and often present antigens that bulge out of the peptide binding cleft. This observation raises the question of whether MHC I presents antigens in a similar way in species with many MHC genes? Here, we present the X-ray structure of MHC I from the great reed warbler Acrocephalus arundinaceus (Acar3) a long-distance migratory songbird. Structural analysis shows that MHC I binds the antigen in a flat conformation due to a sequentially well-conserved restriction point, acting like a pair of tweezers, within the peptide binding grove, created by Arg97 and Arg155. This more stringent antigen presentation by Acar MHC I molecules may partly explain the high MHC gene copy numbers seen in the great reed warbler.


  • Organizational Affiliation
    • Experimental Medical Science, Medical Structural Biology, BMC C13, Lund University, Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 47.34 kDa 
  • Atom Count: 3,221 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 405 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen275Acrocephalus arundinaceusMutation(s): 0 
UniProt
Find proteins for O98187 (Acrocephalus arundinaceus)
Explore O98187 
Go to UniProtKB:  O98187
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO98187
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin122Acrocephalus arundinaceusMutation(s): 0 
Gene Names: B2M
UniProt
Find proteins for A0A076JEK1 (Acrocephalus arundinaceus)
Explore A0A076JEK1 
Go to UniProtKB:  A0A076JEK1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076JEK1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LYS-THR-MET-MET-ALA-HIS-ASP-LEUC [auth K]8LegionellaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.947α = 90
b = 49.038β = 94.69
c = 39.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union679799

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references