2AQ2 | pdb_00002aq2

Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant

• PDB DOI: https://doi.org/10.2210/pdb2AQ2/pdb

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


• Deposited: 2005-08-17 Released: 2006-03-21 
• Deposition Author(s): Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.

Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

(2005) Structure 13: 1775-1787

• PubMed: 16338399 
• DOI: https://doi.org/10.1016/j.str.2005.11.001
• Primary Citation Related Structures: 
  2APB, 2APF, 2APT, 2APV, 2APW, 2APX, 2AQ1, 2AQ2, 2AQ3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.44 kDa 
• Atom Count: 3,024 
• Modeled Residue Count: 344 
• Deposited Residue Count: 349 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR BETA CHAIN V	A	112	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P04213 (Mus musculus) Explore P04213  Go to UniProtKB:  P04213

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin type C-3	B	237	Staphylococcus aureus	Mutation(s): 0  Gene Names: entC3
UniProt
Find proteins for P0A0L5 (Staphylococcus aureus) Explore P0A0L5  Go to UniProtKB:  P0A0L5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth B], E [auth B], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.537	α = 90
b = 96.537	β = 90
c = 92.182	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary