Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.51 kDa 
• Atom Count: 6462 
• Residue Count: 770 
• Unique protein chains: 3

1NAN

MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE

• DOI: 10.2210/pdb1NAN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-11-28 Released: 2003-03-11 
• Deposition Author(s): Reiser, J.-B., Darnault, C., Gregoire, C., Mosser, T., Mazza, G., Kearnay, A., van der Merwe, P.A., Fontecilla-Camps, J.C., Housset, D., Malissen, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 

Literature

CDR3 loop flexibility contributes to the degeneracy of TCR recognition

Reiser, J.-B., Darnault, C., Gregoire, C., Mosser, T., Mazza, G., Kearnay, A., van der Merwe, P.A., Fontecilla-Camps, J.C., Housset, D., Malissen, B.

(2003) Nat Immunol 4: 241-247

• PubMed: 12563259 
• DOI: 10.1038/ni891
• Primary Citation of Related Structures:  
  1NAN, 1NAM


• PubMed Abstract: 
  

T cell receptor (TCR) binding degeneracy lies at the heart of several physiological and pathological phenomena, yet its structural basis is poorly understood. We determined the crystal structure of a complex involving the BM3.3 TCR and an octapeptide (VSV8) bound to the H-2K(b) major histocompatibility complex molecule at a 2.7 A resolution, and compared it with the BM3.3 TCR bound to the H-2K(b) molecule loaded with a peptide that has no primary sequence identity with VSV8. Comparison of these structures showed that the BM3.3 TCR complementarity-determining region (CDR) 3alpha could undergo rearrangements to adapt to structurally different peptide residues. Therefore, CDR3 loop flexibility helps explain TCR binding cross-reactivity.

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Related Citations: 

• A T-Cell Receptor Cdr3Beta Loop Undergoes Conformational Changes of Unprecedented Magnitude Upon Binding to a Peptide/Mhc Class I Complex
  Reiser, J.-B., Gregoire, C., Darnault, C., Mosser, T., Guimezanes, A., Schmitt-Verhulst, A.-M., Fontecilla-Camps, J.C., Mazza, G., Malissen, B., Housset, D.
  (2002) Immunity 16: 345

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Organizational Affiliation: 

Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale J.-P. Ebel, CEA-CNRS-UJF, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	H, L	278	Mus musculus	Mutation(s): 0  Gene Names: H2-K, H2-K1
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	I, P	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pBM1 peptide	M, Q	8	N/A	Mutation(s): 0
Find proteins for Q8CDD8 (Mus musculus) Explore Q8CDD8  Go to UniProtKB:  Q8CDD8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.981	α = 90
b = 88.614	β = 111.6
c = 89.174	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-28 
• Released Date: 2003-03-11 
Deposition Author(s): Reiser, J.-B., Darnault, C., Gregoire, C., Mosser, T., Mazza, G., Kearnay, A., van der Merwe, P.A., Fontecilla-Camps, J.C., Housset, D., Malissen, B.

Revision History 

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance