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- PDB-1ktk: Complex of Streptococcal pyrogenic enterotoxin C (SpeC) with a hu... -

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Basic information

Entry
Database: PDB / ID: 1ktk
TitleComplex of Streptococcal pyrogenic enterotoxin C (SpeC) with a human T cell receptor beta chain (Vbeta2.1)
Components
  • Exotoxin type C
  • T-cell receptor beta chain
KeywordsIMMUNE SYSTEM / Streptococcus / immunity / T cell receptor beta
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / alpha-beta T cell activation / PD-1 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / alpha-beta T cell activation / PD-1 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / adaptive immune response / immune response / extracellular region / membrane / plasma membrane
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / 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 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / 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 constant 1 / Exotoxin type C / Exotoxin type C
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsSundberg, E.J. / Li, H. / Llera, A.S. / McCormick, J.K. / Tormo, J. / Karjalainen, K. / Schlievert, P.M. / 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
DepositionJan 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exotoxin type C
B: Exotoxin type C
C: Exotoxin type C
D: Exotoxin type C
E: T-cell receptor beta chain
F: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)152,4606
Polymers152,4606
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.378, 146.764, 135.690
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Exotoxin type C / pyrogenic exotoxin C / SPE C / SpeC


Mass: 24384.285 Da / Num. of mol.: 4 / Mutation: H35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P13380, UniProt: Q8NKX2*PLUS
#2: Protein T-cell receptor beta chain / TCR beta chain


Mass: 27461.572 Da / Num. of mol.: 2 / Mutation: C13A, C191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850

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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: 3.7 Å3/Da / Density % sol: 66.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 8000, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 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: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 43729 / Num. obs: 36549 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.16 Å / % possible all: 81.9
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / Num. obs: 43729 / % possible obs: 97.8 % / Num. measured all: 158446 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 3→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 256344.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1846 5.1 %RANDOM
Rwork0.326 ---
obs0.326 36547 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 116.651 Å2 / ksol: 0.613989 e/Å3
Displacement parametersBiso mean: 76.1 Å2
Baniso -1Baniso -2Baniso -3
1--27.27 Å20 Å29.8 Å2
2--9.7 Å20 Å2
3---17.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9511 0 0 0 9511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 3→3.16 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 278 5.2 %
Rwork0.364 5036 -
obs--81.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
% reflection Rfree: 4.8 % / Rfactor Rfree: 0.335
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.99
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / Rfactor Rwork: 0.357 / Rfactor obs: 0.357

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