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- PDB-2xna: Crystal structure of the complex between human T cell receptor an... -

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Basic information

Entry
Database: PDB / ID: 2xna
TitleCrystal structure of the complex between human T cell receptor and staphylococcal enterotoxin
Components
  • (T CELL RECEPTOR ...) x 2
  • ENTEROTOXIN H
KeywordsIMMUNE SYSTEM / SUPERANTIGEN
Function / homology
Function and homology information


MHC class II protein binding / 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 / Co-inhibition by PD-1 / T cell receptor binding / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...MHC class II protein binding / 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 / Co-inhibition by PD-1 / T cell receptor binding / 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 / immune response / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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 / : / 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 chain constant / T cell receptor beta constant 1 / Enterotoxin type H
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaline, M. / Rodstrom, K.E.J. / Fischer, G. / Orekhov, V.Y. / Karlsson, B.G. / Lindkvist-Petersson, K.
CitationJournal: Nat.Commun. / Year: 2010
Title: The Structure of Superantigen Complexed with Tcr and Mhc Reveals Novel Insights Into Superantigenic T Cell Activation.
Authors: Saline, M. / Rodstrom, K.E.J. / Fischer, G. / Orekhov, V.Y. / Karlsson, B.G. / Lindkvist-Petersson, K.
History
DepositionJul 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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 C REGION
B: T CELL RECEPTOR BETA-1 CHAIN C REGION
C: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5797
Polymers75,2803
Non-polymers2994
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-29.4 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.692, 49.980, 132.834
Angle α, β, γ (deg.)90.00, 131.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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T CELL RECEPTOR ... , 2 types, 2 molecules AB

#1: Protein T CELL RECEPTOR ALPHA CHAIN C REGION


Mass: 22313.818 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1-95 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRAV27 FUSED TO CONSTANT DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T LYMPHOCYTE / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848
#2: Protein T CELL RECEPTOR BETA-1 CHAIN C REGION


Mass: 27785.787 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1-130 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRBV19 FUSED TO CONSTANT DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T LYMPHOCYTE / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850

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Protein , 1 types, 1 molecules C

#3: Protein ENTEROTOXIN H / SEH / STAPHYLOCOCCAL ENTEROTOXIN H


Mass: 25180.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): UL635 / References: UniProt: P0A0M0

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Non-polymers , 3 types, 253 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCHAIN A RESIDUES 1-109 CONTAINS THE TCR VARIABLE DOMAIN TRAV27. ALPHA CHAIN RESIDUES 96-142 ARE ...CHAIN A RESIDUES 1-109 CONTAINS THE TCR VARIABLE DOMAIN TRAV27. ALPHA CHAIN RESIDUES 96-142 ARE EXCLUDED. CHAIN B RESIDUES 1-114 CONTAINS THE TCR VARIABLE DOMAIN TRBV19. BETA CHAIN RESIDUES 131-177 ARE EXCLUDED. SIGNAL SEQUENCES (RESIDUES C1-24, D1-29) NOT IN CONSTRUCTS.

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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 % / Description: NONE
Crystal growpH: 6.5 / Details: 12% W/V PEG 5000 MME, 0.1 M MES PH 6.5, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 6, 2010 / Details: PT COATED MIRRORS
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→45.65 Å / Num. obs: 52446 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 44.39 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGA CHAINS D, E AND 1HXY CHAIN D

1oga

1hxy


Resolution: 2.1→99.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.267 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26137 2670 5.1 %RANDOM
Rwork0.22256 ---
obs0.22461 49776 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.705 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å2-1.28 Å2
2--0.8 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→99.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 19 249 5430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.957367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45225.056267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92715918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7131526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214196
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.53337
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41725393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7832089
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8444.51974
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 178 -
Rwork0.267 3657 -
obs--98.81 %

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