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- PDB-5fk9: Crystal structure of staphylococcal enterotoxin A F47A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 5fk9
TitleCrystal structure of staphylococcal enterotoxin A F47A mutant in complex with a T cell receptor
Components
  • ENTEROTOXIN TYPE A
  • T CELL RECEPTOR ALPHA CHAIN
  • T CELL RECEPTOR BETA CHAIN
KeywordsIMMUNE SYSTEM / SUPERANTIGEN / STAPHYLCOCOCCAL ENTEROTOXIN / T CELL RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX
Function / homology
Function and homology information


MHC class II protein binding / T cell receptor complex / toxin activity / adaptive immune response / 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 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 / Domain of unknown function (DUF1968) / 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 C1-set domain / 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 alpha variable 22 / V_segment translation product / Enterotoxin type A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K.
CitationJournal: Sci.Rep. / Year: 2016
Title: Two Common Structural Motifs for Tcr Recognition by Staphylococcal Enterotoxins
Authors: Rodstrom, K.E.J. / Regenthal, P. / Bahl, C. / Ford, A. / Baker, D. / Lindkvist-Petersson, K.
History
DepositionOct 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T CELL RECEPTOR ALPHA CHAIN
B: T CELL RECEPTOR BETA CHAIN
C: ENTEROTOXIN TYPE A


Theoretical massNumber of molelcules
Total (without water)77,6323
Polymers77,6323
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-34.9 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.340, 150.440, 39.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein T CELL RECEPTOR ALPHA CHAIN


Mass: 22812.125 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAINS, RESIDUES 1-206
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRAV22 AND CONSTANT DOMAIN TRAC1 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A0B4J277*PLUS
#2: Protein T CELL RECEPTOR BETA CHAIN


Mass: 27765.832 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAINS, RESIDUES 1-243
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRBV7-9 AND CONSTANT DOMAIN TRBC2 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A5A3*PLUS
#3: Protein ENTEROTOXIN TYPE A / SEA


Mass: 27054.209 Da / Num. of mol.: 1 / Fragment: OB DOMAIN AND BETA GRASP DOMAIN, RESIDUES 25-257 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Gene: ENTA / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): UL 635 / References: UniProt: P0A0L2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ...THE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ONLY AVAILABLE FOR THE CONSTANT DOMAIN. ENGINEERED DISULPHIDE BOND BETWEEN THE TRAC AND TRBC DOMAINS. THE STRUCTURE CONTAINS EXTRACELLULAR TCR BETA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ONLY AVAILABLE FOR THE CONSTANT DOMAIN. ENGINEERED DISULPHIDE BOND BETWEEN THE TRAC AND TRBC DOMAINS.

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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: 2.2 Å3/Da / Density % sol: 44.12 % / Description: NONE
Crystal growpH: 8.5
Details: 24% W/V PEG 2000 MME, 0.1 M AMMONIUM CHLORIDE PH 8.5, 0.05 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.09→45.92 Å / Num. obs: 12028 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 83.67 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 3.09→3.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.8 / % possible all: 90.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ESF, 4UDT

1esf

4udt


Resolution: 3.1→45.92 Å / Cor.coef. Fo:Fc: 0.8513 / Cor.coef. Fo:Fc free: 0.8243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.583
RfactorNum. reflection% reflectionSelection details
Rfree0.2908 585 4.93 %RANDOM
Rwork0.2571 ---
obs0.2587 11871 90.69 %-
Displacement parametersBiso mean: 57.87 Å2
Baniso -1Baniso -2Baniso -3
1-5.7157 Å20 Å20 Å2
2--3.9529 Å20 Å2
3----9.6686 Å2
Refine analyzeLuzzati coordinate error obs: 0.671 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 0 4 4771
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.886699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1471SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes750HARMONIC5
X-RAY DIFFRACTIONt_it4890HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.41
X-RAY DIFFRACTIONt_other_torsion21.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion671SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4748SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.4 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3477 128 4.61 %
Rwork0.2776 2647 -
all0.2807 2775 -
obs--90.69 %

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