3V4U

Structure of a monoclonal antibody complexed with its MHC-I antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Peptide-receptive transition state of MHC class I molecules: insight from structure and molecular dynamics.

Mage, M.G.Dolan, M.A.Wang, R.Boyd, L.F.Revilleza, M.J.Robinson, H.Natarajan, K.Myers, N.B.Hansen, T.H.Margulies, D.H.

(2012) J Immunol 189: 1391-1399

  • DOI: 10.4049/jimmunol.1200831
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic ...

    MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed "open" position in the PR transition state to a "closed" position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.


    Organizational Affiliation

    Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. mmage@mail.nih.gov



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 H CHAINH216Mus musculusMutation(s): 0 
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTI-MHC-I MONOCLONAL ANTIBODY, 64-3-7 L CHAINL218Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, L-D alpha chainP9Mus musculusMutation(s): 0 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Explore P01897 
Go to UniProtKB:  P01897
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.14α = 90
b = 40.643β = 103.07
c = 59.069γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references