Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.00 kDa 
• Atom Count: 5091 
• Modelled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 5

1NAM

MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX

• DOI: 10.2210/pdb1NAM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Mus musculus, 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: 2.70 Å
• R-Value Free: 0.298 
• R-Value Work: 0.230 
• R-Value Observed: 0.237 

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: 

• Crystal structure of a T cell receptor bound to an allogeneic MHC molecule
  Reiser, J.-B., Darnault, C., Guimezanes, A., Gregoire, C., Mosser, T., Schmitt-Verhulst, A.-M., Fontecilla-Camps, J.C., Malissen, B., Housset, D., Mazza, G.
  (2000) Nat Immunol 1: 291

• 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

• Crystal Structures of Two Viral Peptides in Complex with Murine MHC Class I H-2Kb
  Fremont, D.H., Matsumura, M., Stura, E.A., Peterson, P.A., Wilson, I.A.
  (1992) Science 257: 919

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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
BM3.3 T Cell Receptor alpha-Chain	A	116	Mus musculus	Mutation(s): 0  Gene Names: TRADV16D, TRAV16
Find proteins for Q5R1F1 (Mus musculus) Explore Q5R1F1  Go to UniProtKB:  Q5R1F1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BM3.3 T Cell Receptor beta-Chain	B	113	Mus musculus	Mutation(s): 0
Find proteins for P04214 (Mus musculus) Explore P04214  Go to UniProtKB:  P04214

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain precursor	H	275	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid	P	8	N/A	Mutation(s): 0
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow)) Explore P11212  Go to UniProtKB:  P11212

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	L	100	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

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.298 
• R-Value Work: 0.230 
• R-Value Observed: 0.237 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.86	α = 90
b = 101.86	β = 90
c = 201.36	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: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary