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- PDB-2xn9: Crystal structure of the ternary complex between human T cell rec... -

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Entry
Database: PDB / ID: 2xn9
TitleCrystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II
Components
  • (T CELL RECEPTOR ...) x 2
  • ENTEROTOXIN H
  • HEMAGGLUTININ
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN,
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN
KeywordsIMMUNE SYSTEM / SUPERANTIGEN / IMMUNORECEPTORS / TERNARY COMPLEX
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / MHC class II protein binding ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / alpha-beta T cell activation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / immunoglobulin complex, circulating / negative regulation of inflammatory response to antigenic stimulus / immunoglobulin receptor binding / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / protein tetramerization / antigen binding / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / toxin activity / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / blood microparticle / host cell surface receptor binding / positive regulation of protein phosphorylation / immune response / apical plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Staphylococcal/streptococcal toxin, bacterial / 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 ...Staphylococcal/streptococcal toxin, bacterial / 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 / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Enterotoxin / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / MHC classes I/II-like antigen recognition protein / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Hemagglutinin / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Enterotoxin type H / Hemagglutinin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 3, 2011Group: Database references / Non-polymer description / 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

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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
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN,
E: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,41511
Polymers120,0236
Non-polymers3915
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-94 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.180, 48.890, 166.720
Angle α, β, γ (deg.)90.00, 113.55, 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 , 3 types, 3 molecules CDE

#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
#4: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN, / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II ALPHA / MHC CLASS II ANTIGEN DRA CHAIN


Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-207
Source method: isolated from a genetically manipulated source
Details: CHAIN DR 0101 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: ANTIGEN PRESENTING CELL / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: P01903
#5: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN / MHC CLASS II ANTIGEN DRB1.1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 30-219
Source method: isolated from a genetically manipulated source
Details: CHAIN DRB1 0101 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: ANTIGEN PRESENTING CELL / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide , 1 types, 1 molecules F

#6: Protein/peptide HEMAGGLUTININ / INFLUENZA HEMAGGLUTININ PEPTIDE


Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-71 / Source method: obtained synthetically / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: A8CDU0, UniProt: Q03909*PLUS

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Non-polymers , 3 types, 285 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 49 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 57 TO CYS
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 B1-24, C1-25, D1-29) NOT IN CONSTRUCTS. SYNTHETIC PEPTIDE F OF 13 RESIDUES, 306-318 OF INFLUENZA HEMAGGLUTININ.

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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: 7
Details: 15% W/V PEG 5000 MME, 0.1 M BIS-TRIS PH 7.0, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 23, 2009 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→42.72 Å / Num. obs: 61858 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 49.17 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 88.8

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Processing

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

1oga

1hxy


Resolution: 2.3→152.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.35 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27236 3148 5.1 %RANDOM
Rwork0.2215 ---
obs0.22414 58700 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å2-1.62 Å2
2--2.02 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→152.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 25 280 8571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.94711751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67151059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5324.579439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.278151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.711551
X-RAY DIFFRACTIONr_chiral_restr0.0960.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216722
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_it0.7941.55250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48828514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87533396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0614.53237
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 211 -
Rwork0.293 3577 -
obs--80.97 %

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