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- PDB-4udu: Crystal structure of staphylococcal enterotoxin E in complex with... -

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Basic information

Entry
Database: PDB / ID: 4udu
TitleCrystal structure of staphylococcal enterotoxin E in complex with a T cell receptor
Components
  • ENTEROTOXIN TYPE E
  • PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION
  • T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION
KeywordsIMMUNE SYSTEM / SUPERANTIGEN / T CELL RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / immune system process / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / immune system process / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / adaptive immune response / 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 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 / T-cell receptor alpha chain, constant domain / 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 C-Type / Immunoglobulin C1-set / 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 / T cell receptor beta constant 2 / T cell receptor alpha chain constant / Enterotoxin type E
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K.
CitationJournal: Plos One / Year: 2015
Title: Structure of Staphylococcal Enterotoxin E in Complex with Tcr Defines the Role of Tcr Loop Positioning in Superantigen Recognition.
Authors: Rodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K.
History
DepositionDec 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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, T-CELL RECEPTOR ALPHA CHAIN C REGION
B: PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION
C: ENTEROTOXIN TYPE E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4966
Polymers77,3853
Non-polymers1113
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-66.3 kcal/mol
Surface area27840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.134, 78.544, 180.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION


Mass: 22812.125 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAIN TRAV22, RESIDUES 1-112, CONSTANT DOMAIN TRAC1, RESIDUES 2-95
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Gene: TRAC, TCRA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P01848, UniProt: A0A0B4J277*PLUS
#2: Protein PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION / V_SEGMENT TRANSLATION PRODUCT


Mass: 27765.832 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAIN TRBV7-9, RESIDUES 20-115, CONSTANT DOMAIN TRBC2, RESIDUES 1-129
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Gene: TCRBV6S4A1, TRBV7-9, TRBC2, TCRBC2 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: A0A5A3, UniProt: A0A5B9
#3: Protein ENTEROTOXIN TYPE E / SEE


Mass: 26806.947 Da / Num. of mol.: 1 / Fragment: OB DOMAIN AND BETA GRASP DOMAIN, RESIDUES 25-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Gene: ENTE / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): UL 635 / References: UniProt: P12993

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Non-polymers , 3 types, 53 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 9
Details: 15% W/V PEG 20000, 0.1 M GLYCINE PH 9.0, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97628
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2012 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.5→47.81 Å / Num. obs: 31731 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 66.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUPERANTIGEN FROM PDB ENTRY 1ESF AND TCR FROM PDB ENTRY 4UDT

1esf

4udt


Resolution: 2.5→32.33 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.8942 / SU R Cruickshank DPI: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.251 / SU Rfree Cruickshank DPI: 0.255
Details: REFMAC 5.7, CNS 1.3, BUSTER 2. DISORDERED REGIONS WERE OMITTED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1567 5.04 %RANDOM
Rwork0.2463 ---
obs0.2467 31093 97.43 %-
Displacement parametersBiso mean: 66.02 Å2
Baniso -1Baniso -2Baniso -3
1--15.4077 Å20 Å20 Å2
2--1.094 Å20 Å2
3---14.3137 Å2
Refine analyzeLuzzati coordinate error obs: 0.521 Å
Refinement stepCycle: LAST / Resolution: 2.5→32.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 3 50 4915
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074981HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.946785HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1609SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes744HARMONIC5
X-RAY DIFFRACTIONt_it4981HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion21.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion662SEMIHARMONIC5
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_contact5081SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3596 131 5.26 %
Rwork0.3107 2359 -
all0.3132 2490 -
obs--97.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76841.43812.66573.14422.14282.9714-0.004-0.1358-0.1381-0.1151-0.06130.10030.19580.13780.0653-0.1027-0.08650.10210.1757-0.0065-0.1433-33.28191.7824-12.9176
22.37241.59771.51191.9180.88140.94580.034-0.1375-0.13670.0884-0.03930.12030.09050.11190.0053-0.04820.03490.1335-0.0696-0.0539-0.0711-27.339810.2004-28.7462
32.68690.3527-0.71162.4664-0.3072.8188-0.0090.05910.3586-0.0707-0.0938-0.0133-0.30770.12470.1028-0.06880.0751-0.0168-0.13030.0569-0.10914.104539.9656-22.6509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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