2ICW

Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule

• PDB DOI: https://doi.org/10.2210/pdb2ICW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Metamycoplasma arthritidis, Mus musculus
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-09-13 Released: 2007-03-20 
• Deposition Author(s): Wang, L., Zhao, Y., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.288 
• R-Value Work: 0.242 
• R-Value Observed: 0.242 

Starting Models: experimental

Literature

Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC.

Wang, L., Zhao, Y., Li, Z., Guo, Y., Jones, L.L., Kranz, D.M., Mourad, W., Li, H.

(2007) Nat Struct Mol Biol 14: 169-171

• PubMed: 17220897 
• DOI: https://doi.org/10.1038/nsmb1193
• Primary Citation of Related Structures:  
  2ICW


• PubMed Abstract: 
  

  'Superantigens' (SAgs) trigger the massive activation of T cells by simultaneous interactions with MHC and TCR receptors, leading to human diseases. Here we present the first crystal structure, at 2.5-A resolution, of a complete ternary complex between a SAg and its two receptors, HLA-DR1/HA and TCR. The most striking finding is that the SAg Mycoplasma arthritidis mitogen, unlike others, has direct contacts not only with TCR Vbeta but with TCR Valpha.

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Organizational Affiliation: 

Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 188.4 kDa 
• Atom Count: 13,464 
• Modelled Residue Count: 1,622 
• Deposited Residue Count: 1,636 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, D	179	Homo sapiens	Mutation(s): 3  Gene Names: HLA-DRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
haemagglutinin peptide	C, F	13	N/A	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycoplasma arthritidis mitogen	G, H	213	Metamycoplasma arthritidis	Mutation(s): 0
UniProt
Find proteins for Q48898 (Metamycoplasma arthritidis) Explore Q48898  Go to UniProtKB:  Q48898

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor alpha chain V	I, K	110	Mus musculus	Mutation(s): 2
UniProt
Find proteins for P01738 (Mus musculus) Explore P01738  Go to UniProtKB:  P01738

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta chain V	J, L	113	Mus musculus	Mutation(s): 3
UniProt
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.288 
• R-Value Work: 0.242 
• R-Value Observed: 0.242 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.516	α = 110.27
b = 86.822	β = 92.32
c = 116.981	γ = 107.87

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Wang, L., Zhao, Y., Li, H.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection