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- PDB-4ozi: S2 protein complex -

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Basic information

Entry
Database: PDB / ID: 4ozi
TitleS2 protein complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • (T-cell receptor, s2, ...) x 2
  • deamidated Gliadin-alpha1 peptide
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX
Function / homology
Function and homology information


nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / transport vesicle membrane / 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 ...nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / transport vesicle membrane / 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 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / metal ion binding / membrane / plasma membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / : / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / 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) ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / : / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / 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) / 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 / : / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / Alpha/beta-gliadin A-II / TRA@ protein / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsPetersen, J. / Reid, H.H. / Rossjohn, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease.
Authors: Petersen, J. / Montserrat, V. / Mujico, J.R. / Loh, K.L. / Beringer, D.X. / van Lummel, M. / Thompson, A. / Mearin, M.L. / Schweizer, J. / Kooy-Winkelaar, Y. / van Bergen, J. / Drijfhout, J. ...Authors: Petersen, J. / Montserrat, V. / Mujico, J.R. / Loh, K.L. / Beringer, D.X. / van Lummel, M. / Thompson, A. / Mearin, M.L. / Schweizer, J. / Kooy-Winkelaar, Y. / van Bergen, J. / Drijfhout, J.W. / Kan, W.T. / La Gruta, N.L. / Anderson, R.P. / Reid, H.H. / Koning, F. / Rossjohn, J.
History
DepositionFeb 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Data collection
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Apr 22, 2015Group: Database references
Revision 1.5Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 6, 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: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T-cell receptor, s2, alpha chain
F: T-cell receptor, s2, beta chain
G: T-cell receptor, s2, alpha chain
H: T-cell receptor, s2, beta chain
I: deamidated Gliadin-alpha1 peptide
J: deamidated Gliadin-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,92014
Polymers195,39810
Non-polymers5234
Water00
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
G: T-cell receptor, s2, alpha chain
H: T-cell receptor, s2, beta chain
J: deamidated Gliadin-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9607
Polymers97,6995
Non-polymers2612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: HLA class II histocompatibility antigen, DQ beta 1 chain
E: T-cell receptor, s2, alpha chain
F: T-cell receptor, s2, beta chain
I: deamidated Gliadin-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9607
Polymers97,6995
Non-polymers2612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)233.027, 142.239, 101.090
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HLA class II histocompatibility antigen, DQ ... , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 21517.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01909
#2: Protein HLA class II histocompatibility antigen, DQ beta 1 chain / MHC class II antigen


Mass: 24361.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5Y7D3

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T-cell receptor, s2, ... , 2 types, 4 molecules EGFH

#3: Protein T-cell receptor, s2, alpha chain


Mass: 22915.309 Da / Num. of mol.: 2 / Mutation: T174C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2YD82*PLUS
#4: Protein T-cell receptor, s2, beta chain


Mass: 27447.760 Da / Num. of mol.: 2 / Mutation: C202A, S184C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01850*PLUS

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Protein/peptide / Sugars / Non-polymers , 3 types, 6 molecules IJ

#5: Protein/peptide deamidated Gliadin-alpha1 peptide


Mass: 1456.596 Da / Num. of mol.: 2 / Mutation: Q6E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04722*PLUS
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsThe authors state that there are mutations T174C in T-cell receptor, s2, alpha chain, S184C and ...The authors state that there are mutations T174C in T-cell receptor, s2, alpha chain, S184C and C202A in T-cell receptor, s2, beta chain, Q6E in deamidated Gliadin-alpha1 peptide.

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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: 4.03 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→46.85 Å / Num. obs: 49219 / % possible obs: 96.06 % / Redundancy: 1.9 % / Biso Wilson estimate: 61.28 Å2 / Rmerge(I) obs: 0.1593 / Net I/σ(I): 4.24

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 3.2→46.85 Å / Cor.coef. Fo:Fc: 0.8238 / Cor.coef. Fo:Fc free: 0.7865 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.344 / SU Rfree Blow DPI: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 2543 5.17 %RANDOM
Rwork0.2125 ---
obs0.2141 49219 96.05 %-
Displacement parametersBiso mean: 58.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.0495 Å20 Å2-4.8438 Å2
2--12.7696 Å20 Å2
3----8.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.583 Å
Refinement stepCycle: final / Resolution: 3.2→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12819 0 30 0 12849
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913203HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9718023HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5892SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes328HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1911HARMONIC5
X-RAY DIFFRACTIONt_it13203HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion3.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1738SEMIHARMONIC5
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_contact13561SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2792 180 4.9 %
Rwork0.2323 3493 -
all0.2346 3673 -
obs--96.05 %
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)
11.38310.32370.47283.37620.51354.49320.03460.203-0.1052-0.1069-0.22080.11090.250.16610.18620.28320.02510.0781-0.23460.0104-0.0616238.7883-27.8551118.7705
21.7754-0.16961.8252.7966-0.312.7466-0.0073-0.0811-0.03170.1215-0.25410.78320.1937-0.41740.26150.1182-0.07040.1578-0.1588-0.1556-0.0133223.8974-20.4165123.2848
32.5207-0.073-0.95852.66950.00822.82330.1788-0.03560.03220.3492-0.2170.07-0.1752-0.02770.03820.2852-0.01610.001-0.1889-0.0097-0.1327238.810925.1505112.0592
44.0471.4855-1.56133.0318-0.71221.74590.01680.42750.0245-0.1247-0.05550.4549-0.1157-0.26930.03870.21490.1431-0.1745-0.136-0.1013-0.2196230.162816.406899.9979
53.0238-0.2526-1.36791.2604-0.01411.5911-0.0380.0243-0.085-0.2168-0.0027-0.1876-0.0189-0.0040.04070.3817-0.0127-0.0172-0.2239-0.02130.0472285.00967.942379.1706
62.3706-0.085-1.08771.71970.21280.312-0.0962-0.30780.23160.11260.1029-0.360.01870.0926-0.00670.2795-0.0274-0.0838-0.09270.06720.0185291.544521.809291.9124
71.0223-0.18512.01081.4690.35065.5621-0.1101-0.0291-0.10150.05140.0888-0.11550.0057-0.03260.02120.30140.04020.0904-0.21750.0377-0.0309250.9842-10.3266174.1627
80.8895-0.44841.41261.09780.44522.8210.08560.3164-0.2057-0.00610.0337-0.4260.20520.3981-0.11940.27280.0101-0.0694-0.16360.15010.0823265.1739-23.3983169.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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