Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48180.65 
• Atom Count: 3353 
• Residue Count: 442 
• Unique protein chains: 3

3UYR

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

• DOI: 10.2210/pdb3UYR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus


• Deposited: 2011-12-06 Released: 2012-07-25 
• Deposition Author(s): Margulies, D.H., Mage, M.G., Wang, R., Natarajan, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 

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

• PubMed: 22753930 
• DOI: 10.4049/jimmunol.1200831
• Primary Citation of Related Structures:  
  3V52, 3V4U, 3UO1


• 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 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.

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Organizational Affiliation: 

Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
antibody Fab heavy chain	H	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
antibody Fab light chain	L	218	Mus musculus	Mutation(s): 0  Gene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus) Go to UniProtKB:  A2NHM3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
H-2 class I histocompatibility antigen, L-D alpha chain	P	8	Mus musculus	Mutation(s): 0  Gene Names: H2-L
Find proteins for P01897 (Mus musculus) Go to UniProtKB:  P01897

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	L	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 193.524	α = 90.00
b = 40.423	β = 102.74
c = 59.265	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data collection
PHENIX	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-06 
• Released Date: 2012-07-25 
• Deposition Author(s): Margulies, D.H., Mage, M.G., Wang, R., Natarajan, K.

Revision History 

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