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- PDB-2aq2: Crystal structure of T-cell receptor V beta domain variant comple... -

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Basic information

Entry
Database: PDB / ID: 2aq2
TitleCrystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant
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: 1.8 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAIN A AT THE TIME OF ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAIN A AT THE TIME OF PROCESSING THIS ENTRY. THE FIVE SEC3 WILD TYPE RESIDUES AT POSITIONS 102-106 (GKVTG) IN CHAIN B ARE REPLACED BY THREE RESIDUES (WWP).

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,44011
Polymers39,8252
Non-polymers6159
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-97 kcal/mol
Surface area15970 Å2
MethodPISA
2
B: Enterotoxin type C-3
hetero molecules

A: T-CELL RECEPTOR BETA CHAIN V


Theoretical massNumber of molelcules
Total (without water)40,44011
Polymers39,8252
Non-polymers6159
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
Buried area2840 Å2
ΔGint-104 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.537, 96.537, 92.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-CELL RECEPTOR BETA CHAIN V


Mass: 12176.396 Da / Num. of mol.: 1 / Mutation: G17E,A52V,S54N,K66E,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: 27649.002 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 240 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulfate, 0.1 M Tris, 0.3 % 1,6-diaminohexane, 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 6, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Number: 44916 / Rmerge(I) obs: 0.052 / Χ2: 1.631 / D res high: 1.8 Å / D res low: 50 Å / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.110.0352.5173.6
3.083.8899.610.0442.9053.6
2.693.0899.810.0562.3083.7
2.442.6999.910.0651.5513.7
2.272.4499.710.0791.3493.7
2.132.2799.610.0981.313.7
2.032.1399.610.1341.2013.7
1.942.0399.410.1871.0523.7
1.861.9499.110.2811.0773.6
1.81.8694.710.3690.9453.2
ReflectionResolution: 1.8→50 Å / Num. obs: 44916 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Χ2: 1.631
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.369 / Num. measured obs: 4264 / Χ2: 0.945 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.149 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2257 5 %RANDOM
Rwork0.185 ---
all0.186 45302 --
obs0.185 44890 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 29 231 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222848
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.953851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48925.248141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022161
X-RAY DIFFRACTIONr_nbd_refined0.2280.21219
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2242
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_mcbond_it1.0341.51704
X-RAY DIFFRACTIONr_mcangle_it1.93322750
X-RAY DIFFRACTIONr_scbond_it2.9131189
X-RAY DIFFRACTIONr_scangle_it4.5924.51101
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 167 -
Rwork0.252 2922 -
all-3089 -
obs--93.04 %

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