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- PDB-2ij0: Structural basis of T cell specificity and activation by the bact... -

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Basic information

Entry
Database: PDB / ID: 2ij0
TitleStructural basis of T cell specificity and activation by the bacterial superantigen toxic shock syndrome toxin-1
Components
  • Toxic shock syndrome toxin-1
  • penultimate affinity-matured variant of hVbeta 2.1, D10
KeywordsPROTEIN BINDING / Superantigen / Protein-protein interaction
Function / homology
Function and homology information


toxin activity / cell surface receptor signaling pathway / extracellular region / plasma membrane
Similarity search - Function
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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 variable 20-1 / Toxic shock syndrome toxin-1 / : / Toxic shock syndrome toxin-1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMoza, B. / Varma, A.K. / Buonpane, R.A. / Zhu, P. / Herfst, C.A. / Nicholson, M.J. / Wilbuer, A.K. / Nulifer, S. / Wucherpfenning, K.W. / McCormick, J.K. ...Moza, B. / Varma, A.K. / Buonpane, R.A. / Zhu, P. / Herfst, C.A. / Nicholson, M.J. / Wilbuer, A.K. / Nulifer, S. / Wucherpfenning, K.W. / McCormick, J.K. / Kranz, D.M. / Sundberg, E.J.
CitationJournal: Embo J. / Year: 2007
Title: Structural basis of T-cell specificity and activation by the bacterial superantigen TSST-1.
Authors: Moza, B. / Varma, A.K. / Buonpane, R.A. / Zhu, P. / Herfst, C.A. / Nicholson, M.J. / Wilbuer, A.K. / Seth, N.P. / Wucherpfennig, K.W. / McCormick, J.K. / Kranz, D.M. / Sundberg, E.J.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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: Toxic shock syndrome toxin-1
E: penultimate affinity-matured variant of hVbeta 2.1, D10
B: Toxic shock syndrome toxin-1
C: penultimate affinity-matured variant of hVbeta 2.1, D10


Theoretical massNumber of molelcules
Total (without water)69,8084
Polymers69,8084
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.898, 68.372, 53.549
Angle α, β, γ (deg.)90.000, 106.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-146-

HOH

DetailsThe biological assembly is dimer in the asymmetric unit

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Components

#1: Protein Toxic shock syndrome toxin-1


Mass: 22103.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q7A4K7, UniProt: P06886*PLUS
#2: Protein penultimate affinity-matured variant of hVbeta 2.1, D10


Mass: 12800.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT 7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5W0G6, UniProt: A0A5B4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2 M Magnesium Acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.978 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 32180 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rsym value: 0.074 / Net I/σ(I): 21.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1454 4.6 %4.6%
Rwork0.242 ---
all-32180 --
obs-29267 92.6 %-
Solvent computationBsol: 35.956 Å2
Displacement parametersBiso mean: 45.922 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4893 0 0 237 5130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3581.5
X-RAY DIFFRACTIONc_scbond_it1.6612
X-RAY DIFFRACTIONc_mcangle_it2.2932
X-RAY DIFFRACTIONc_scangle_it2.4992.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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