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- PDB-4ozh: S16 protein complex -

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Basic information

Entry
Database: PDB / ID: 4ozh
TitleS16 protein complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • (T-cell receptor, s16, ...) x 2
  • Gliadin-alpha2 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: 2.8 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 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...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 / 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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 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 1.6Oct 23, 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, s16, alpha chain
F: T-cell receptor, s16, beta chain
G: T-cell receptor, s16, alpha chain
H: T-cell receptor, s16, beta chain
I: Gliadin-alpha2 peptide
J: Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,17314
Polymers193,46910
Non-polymers7044
Water72140
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, s16, alpha chain
H: T-cell receptor, s16, beta chain
J: Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2178
Polymers96,7345
Non-polymers4823
Water724
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, s16, alpha chain
F: T-cell receptor, s16, beta chain
I: Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9566
Polymers96,7345
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)261.569, 57.870, 137.411
Angle α, β, γ (deg.)90.00, 114.05, 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, s16, ... , 2 types, 4 molecules EGFH

#3: Protein T-cell receptor, s16, alpha chain


Mass: 22563.098 Da / Num. of mol.: 2 / Mutation: T176C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hi5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2YD82*PLUS
#4: Protein T-cell receptor, s16, beta chain


Mass: 26911.725 Da / Num. of mol.: 2 / Mutation: C202A, S184C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hi5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01850*PLUS

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Protein/peptide / Sugars , 2 types, 5 molecules IJ

#5: Protein/peptide Gliadin-alpha2 peptide


Mass: 1380.500 Da / Num. of mol.: 2
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.: 3 / 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

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Non-polymers , 2 types, 41 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe authors state that there are mutations T176C in T-cell receptor, s16, alpha chain, C202A, S184C ...The authors state that there are mutations T176C in T-cell receptor, s16, alpha chain, C202A, S184C in T-cell receptor, s16, beta chain.

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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: 2.45 Å3/Da / Density % sol: 49.89 %
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: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→40.99 Å / Num. obs: 43700 / % possible obs: 93.22 % / Redundancy: 2 % / Biso Wilson estimate: 76.05 Å2 / Rmerge(I) obs: 0.04927 / Net I/σ(I): 2

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.8982 / Cor.coef. Fo:Fc free: 0.8859 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 2205 5.05 %RANDOM
Rwork0.2264 ---
obs0.2273 43700 93.09 %-
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-4.9264 Å20 Å24.73 Å2
2---6.2576 Å20 Å2
3---1.3312 Å2
Refine analyzeLuzzati coordinate error obs: 0.473 Å
Refinement stepCycle: 1 / Resolution: 2.8→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12735 0 43 40 12818
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813120HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8917904HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5898SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes331HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1900HARMONIC5
X-RAY DIFFRACTIONt_it13120HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.01
X-RAY DIFFRACTIONt_other_torsion3.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1728SEMIHARMONIC5
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_contact13409SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2548 126 5.35 %
Rwork0.2708 2227 -
all0.2699 2353 -
obs--93.09 %
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)
11.6896-0.01622.08740.02020.2752.4602-0.06230.1778-0.04950.0232-0.00270.03470.1215-0.04570.0650.0637-0.0260.0529-0.01970.09490.039827.5786-20.9858199.0694
21.2532-0.32041.3490.0016-0.27851.32140.05230.4967-0.1562-0.07570.08980.0845-0.0520.2083-0.14210.05960.0020.1316-0.0379-0.19690.220132.8451-38.2668189.3565
31.34850.01460.03822.0512-0.59182.59960.07720.1088-0.4583-0.0803-0.1419-0.12720.49740.41690.0647-0.36850.097-0.008-0.13590.0319-0.249336.2753-61.4544240.8605
41.773-0.0401-0.28221.2835-1.24794.5405-0.09440.0476-0.0080.1607-0.04350.0575-0.17950.34160.138-0.4759-0.05170.0065-0.24350.0137-0.332837.5487-47.1727250.1728
51.13110.15331.061600.07451.88190.06220.56970.13680.15020.02480.0930.03680.2566-0.087-0.07240.22010.02960.37460.1020.4906-5.1497-32.437128.069
60.996-0.25190.70630.0015-0.24171.1924-0.03090.4370.17030.0602-0.1319-0.14010.0841-0.03170.16280.1746-0.05160.17960.4487-0.0690.2701-9.7337-15.9489127.61
71.06270.4556-0.00861.17330.12844.08460.0341-0.03690.00150.0621-0.1319-0.3202-0.31150.44290.0978-0.3158-0.0541-0.0278-0.40370.0078-0.1053-2.5319-17.2069185.2738
81.0643-0.36-0.1880.98580.00482.8698-0.1009-0.0377-0.22370.0439-0.0701-0.13350.32860.31620.1711-0.3174-0.0390.022-0.45670.0442-0.1249-4.8507-37.7535186.4072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ C|* }
2X-RAY DIFFRACTION2{ D|* }
3X-RAY DIFFRACTION3{ A|* }
4X-RAY DIFFRACTION4{ B|* }
5X-RAY DIFFRACTION5{ G|* }
6X-RAY DIFFRACTION6{ H|* }
7X-RAY DIFFRACTION7{ E|* }
8X-RAY DIFFRACTION8{ F|* }

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