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- PDB-1l0x: TCR beta chain complexed with streptococcal superantigen SpeA -

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Basic information

Entry
Database: PDB / ID: 1l0x
TitleTCR beta chain complexed with streptococcal superantigen SpeA
Components
  • 14.3.d T cell receptor beta chain
  • Exotoxin type A
KeywordsIMMUNE SYSTEM / TCR / superantigen
Function / homology
Function and homology information


alpha-beta T cell receptor complex / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / toxin activity / antibacterial humoral response / blood microparticle / extracellular exosome / extracellular region
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell receptor beta-2 chain C region / Exotoxin type A / Exotoxin type A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, H. / Sundberg, E.J. / Mariuzza, R.A.
CitationJournal: Structure / Year: 2002
Title: Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes.
Authors: Sundberg, E.J. / Li, H. / Llera, A.S. / McCormick, J.K. / Tormo, J. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A.
History
DepositionFeb 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns ...refine / reflns / reflns_shell / struct_site
Item: _refine.ls_percent_reflns_obs / _reflns.percent_possible_obs ..._refine.ls_percent_reflns_obs / _reflns.percent_possible_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.percent_possible_all / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Chains A and C are not D10 TCR, genbank entry AAB41230. They are rather 14.3.d TCR, whose ...SEQUENCE Chains A and C are not D10 TCR, genbank entry AAB41230. They are rather 14.3.d TCR, whose sequence has not been deposited. The two are slightly different and hence give rise to the four SEQADV.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14.3.d T cell receptor beta chain
B: Exotoxin type A
C: 14.3.d T cell receptor beta chain
D: Exotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0217
Polymers104,7454
Non-polymers2763
Water3,261181
1
A: 14.3.d T cell receptor beta chain
B: Exotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4653
Polymers52,3722
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14.3.d T cell receptor beta chain
D: Exotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5574
Polymers52,3722
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.400, 83.250, 93.583
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 14.3.d T cell receptor beta chain


Mass: 26568.490 Da / Num. of mol.: 2 / Mutation: N24Q, N74Q, N121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): J558L / Production host: Mus musculus (house mouse) / References: UniProt: P01851
#2: Protein Exotoxin type A / Scarlet fever toxin / Erythrogenic toxin / SPE A


Mass: 25803.932 Da / Num. of mol.: 2 / Mutation: C90S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P08095, UniProt: P0DJY7*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
215 %PEG80001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→40.78 Å / Num. all: 38028 / Num. obs: 26926 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.99 % / Biso Wilson estimate: 61.66 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2696 / Rsym value: 0.373 / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.1 % / Num. measured all: 80520
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BEC and 1B1Z

1bec

1b1z


Resolution: 2.8→40.78 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1326 -RANDOM
Rwork0.232 ---
all-27196 --
obs-26924 99 %-
Refinement stepCycle: LAST / Resolution: 2.8→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7124 0 18 181 7323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.007
Refinement
*PLUS
% reflection Rfree: 4.9 % / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.459 / Rfactor Rwork: 0.397 / Rfactor obs: 0.397

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