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- PDB-1jck: T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SEC3 SUPERANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1jck
TitleT-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SEC3 SUPERANTIGEN
Components
  • 14.3.D T CELL ANTIGEN RECEPTOR
  • STAPHYLOCOCCAL ENTEROTOXIN C3
KeywordsCOMPLEX (TOXIN/RECEPTOR) / T-CELL / RECEPTOR / TRANSMEMBRANE / GLYCOPROTEIN / ENTEROTOXIN / TOXIN / SUPERANTIGEN / COMPLEX (TOXIN-RECEPTOR) / COMPLEX (TOXIN-RECEPTOR) complex
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Enterotoxin type C-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFields, B.A. / Mariuzza, R.A.
Citation
Journal: Nature / Year: 1996
Title: Crystal structure of a T-cell receptor beta-chain complexed with a superantigen.
Authors: Fields, B.A. / Malchiodi, E.L. / Li, H. / Ysern, X. / Stauffacher, C.V. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of the Beta Chain of a T Cell Antigen Receptor
Authors: Bentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A.
#2: Journal: J.Exp.Med. / Year: 1995
Title: Superantigen Binding to a T Cell Receptor Beta Chain of Known Three-Dimensional Structure
Authors: Malchiodi, E.L. / Eisenstein, E. / Fields, B.A. / Ohlendorf, D.H. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A.
#3: Journal: Science / Year: 1995
Title: Crystal Structure of the V Alpha Domain of a T Cell Antigen Receptor
Authors: Fields, B.A. / Ober, B. / Malchiodi, E.L. / Lebedeva, M.I. / Braden, B.C. / Ysern, X. / Kim, J.K. / Shao, X. / Ward, E.S. / Mariuzza, R.A.
History
DepositionOct 22, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 ANTIGEN RECEPTOR
B: STAPHYLOCOCCAL ENTEROTOXIN C3
C: 14.3.D T CELL ANTIGEN RECEPTOR
D: STAPHYLOCOCCAL ENTEROTOXIN C3


Theoretical massNumber of molelcules
Total (without water)108,4654
Polymers108,4654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.400, 87.600, 71.400
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (1), (-1) / Vector: 50.4831, 60.5087)

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Components

#1: Protein 14.3.D T CELL ANTIGEN RECEPTOR


Mass: 26568.490 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Mutation: N24Q, N74Q, N121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: GenBank: 1791255
#2: Protein STAPHYLOCOCCAL ENTEROTOXIN C3 / SEC3


Mass: 27664.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FRI913 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: SOLUTION OF 20% PEG1000, 0.1M MGCL2, 0.025% AGAROSE, 0.1M TRIS-HCL PH 6.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION (10MG/ML IN 20MM TRIS-HCL, 25MM NACL, PH 7.5). HANGING DROP METHOD., ...Details: SOLUTION OF 20% PEG1000, 0.1M MGCL2, 0.025% AGAROSE, 0.1M TRIS-HCL PH 6.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION (10MG/ML IN 20MM TRIS-HCL, 25MM NACL, PH 7.5). HANGING DROP METHOD., vapor diffusion - hanging drop
PH range: 6.5-7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.5-10.5 %PEG10001drop
20.05 M1dropMgCl2
30.0125 %agarose1drop
40.05 MTris-HCl1drop
55 mg/mlprotain1drop
619-21 %PEG10001reservoir
70.1 M1reservoirMgCl2
80.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionHighest resolution: 3.5 Å / Num. obs: 11314 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.8
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.7 / % possible all: 81.3
Reflection
*PLUS
Num. measured all: 57553
Reflection shell
*PLUS
% possible obs: 81.3 %

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Processing

Software
NameVersionClassification
HKL/DENZOdata collection
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYSTAL STRUCTURES OF SEC3 AND TCR BETA

Resolution: 3.5→8 Å / Isotropic thermal model: TWO B-FACTORS PER RESIDUE / Cross valid method: FREE R / σ(F): 1
Details: ATOMS ASSIGNED ZERO OCCUPANCY WERE NOT PRESENT IN ELECTRON DENSITY PRESUMABLY BECAUSE OF THE LOW RESOLUTION. HOWEVER, THESE ATOMS WERE LOCATED IN THE CRYSTAL STRUCTURES OF THE UNCOMPLEXED ...Details: ATOMS ASSIGNED ZERO OCCUPANCY WERE NOT PRESENT IN ELECTRON DENSITY PRESUMABLY BECAUSE OF THE LOW RESOLUTION. HOWEVER, THESE ATOMS WERE LOCATED IN THE CRYSTAL STRUCTURES OF THE UNCOMPLEXED COMPONENTS AND ARE THEREFORE INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1157 12 %RANDOM
Rwork0.238 ---
obs0.238 9604 82.8 %-
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 0 0 3770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT TWO-FOLD
LS refinement shellResolution: 3.5→3.57 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.339 74 13 %
Rwork0.285 495 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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