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- PDB-2nts: Crystal Structure of SEK-hVb5.1 -

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Basic information

Entry
Database: PDB / ID: 2nts
TitleCrystal Structure of SEK-hVb5.1
Components
  • Staphylococcal enterotoxin K
  • TRBC1 protein
KeywordsTOXIN/IMMUNE SYSTEM / superantigen / T cell receptor / TOXIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


alpha-beta 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 / : / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway ...alpha-beta 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 / : / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 ...Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
EntK / T cell receptor beta constant 1 / Staphylococcal enterotoxin / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGunther, S. / Varma, A.K. / Moza, B. / Sundberg, E.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A novel loop domain in superantigens extends their T cell receptor recognition site
Authors: Gunther, S. / Varma, A.K. / Moza, B. / Kasper, K.J. / Wyatt, A.W. / Zhu, P. / Rahman, A.K. / Li, Y. / Mariuzza, R.A. / McCormick, J.K. / Sundberg, E.J.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: TRBC1 protein
A: Staphylococcal enterotoxin K


Theoretical massNumber of molelcules
Total (without water)52,2152
Polymers52,2152
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.591, 108.031, 128.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRBC1 protein / TRBV5-4 protein


Mass: 27135.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8N2T6, UniProt: P01850*PLUS
#2: Protein Staphylococcal enterotoxin K


Mass: 25079.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: COL / Gene: sek / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q5HHK0, UniProt: O54476*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9779 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 21526 / Num. obs: 21526 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rsym value: 0.087 / Net I/σ(I): 25.9

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB models 2ICI and 1ZGL

2ici

1zgl


Resolution: 2.4→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1010 4.7 %random
Rwork0.219 ---
all-20757 --
obs-20757 96.2 %-
Solvent computationBsol: 25.105 Å2
Displacement parametersBiso mean: 39.129 Å2
Baniso -1Baniso -2Baniso -3
1--10.408 Å20 Å20 Å2
2--6.181 Å20 Å2
3---4.227 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 0 152 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007152
X-RAY DIFFRACTIONc_angle_deg1.6868
X-RAY DIFFRACTIONc_mcbond_it1.3391.5
X-RAY DIFFRACTIONc_scbond_it1.7662
X-RAY DIFFRACTIONc_mcangle_it2.2812
X-RAY DIFFRACTIONc_scangle_it2.6332.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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