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- PDB-2aq3: Crystal structure of T-cell receptor V beta domain variant comple... -

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Basic information

Entry
Database: PDB / ID: 2aq3
TitleCrystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3
Components
  • Enterotoxin type C-3
  • T-cell receptor beta chain V
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR V BETA DOMAIN / STAPHLOCOCCAL ENTEROTOXIN C3 / COMPLEX STRUCTURE
Function / homology
Function and homology information


T cell receptor complex / toxin activity / adaptive immune response / cell surface receptor signaling pathway / extracellular region / metal ion binding / 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 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 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell receptor beta chain V region C5 / Enterotoxin type C-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J.
CitationJournal: Structure / Year: 2005
Title: Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.
Authors: Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 600HETEROGEN PORTIONS OF THE DENSITY WAS COMPRISED OF PEG BUT THE COMPLETE MOLECULE COULD NOT BE TRACED.
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAINS A, C, E and G AT THE ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAINS A, C, E and G AT THE TIME OF PROCESSING THIS ENTRY. TWO SEC3 WILD TYPE RESIDUES AT POSITIONS 100 AND 101 IN THE SEQUENCE DATABASE REFERENCE (NV) WERE REMOVED IN CHAINS B, D, F AND H.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell receptor beta chain V
B: Enterotoxin type C-3
C: T-cell receptor beta chain V
D: Enterotoxin type C-3
E: T-cell receptor beta chain V
F: Enterotoxin type C-3
G: T-cell receptor beta chain V
H: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)158,1258
Polymers158,1258
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.160, 70.460, 98.370
Angle α, β, γ (deg.)74.18, 75.76, 88.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
T-cell receptor beta chain V


Mass: 12121.383 Da / Num. of mol.: 4 / Mutation: G17E, L81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04213
#2: Protein
Enterotoxin type C-3 / SEC3


Mass: 27409.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M tri-ammonium citrate, 0.3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 63758 / % possible obs: 73.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.4 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.3→2.36 Å / % possible all: 73.66

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.872 / SU B: 13.176 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron densities in a few regions, some adjacent residues in the structure appear to be linked by long C-N linkages. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron densities in a few regions, some adjacent residues in the structure appear to be linked by long C-N linkages. These include G63 and Y65 in chains A, C, E; residues Y101 and F108 in chains A, C, E; residues V101 and V102 in chain H.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3394 5.1 %RANDOM
Rwork0.206 ---
all0.212 ---
obs0.209 63758 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.433 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å2-1.17 Å20.63 Å2
2--0.57 Å20.54 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10965 0 0 198 11163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.02211296
X-RAY DIFFRACTIONr_angle_refined_deg3.5311.96215201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7851357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16925.238546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.317151968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2041532
X-RAY DIFFRACTIONr_chiral_restr0.2240.21604
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.028524
X-RAY DIFFRACTIONr_nbd_refined0.320.25354
X-RAY DIFFRACTIONr_nbtor_refined0.3430.27057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.2554
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.25
X-RAY DIFFRACTIONr_mcbond_it1.7951.57229
X-RAY DIFFRACTIONr_mcangle_it2.865210965
X-RAY DIFFRACTIONr_scbond_it4.48135030
X-RAY DIFFRACTIONr_scangle_it6.2244.54236
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 180 -
Rwork0.286 3699 -
all-3879 -
obs--73.66 %

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