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- PDB-4ozf: JR5.1 protein complex -

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Basic information

Entry
Database: PDB / ID: 4ozf
TitleJR5.1 protein complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • (T-CELL RECEPTOR, JR5.1 ...) x 2
  • deamidated 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 / PD-1 signaling ...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 / PD-1 signaling / trans-Golgi network membrane / MHC class II antigen presentation / lumenal side of endoplasmic reticulum membrane / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi membrane / membrane / metal ion binding / 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 subtype / Immunoglobulin / 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 / 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: 2.7 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 15, 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: 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_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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
G: T-CELL RECEPTOR, JR5.1 ALPHA CHAIN
H: T-CELL RECEPTOR, JR5.1 BETA CHAIN
J: deamidated Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4987
Polymers97,0565
Non-polymers4422
Water4,179232
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.930, 84.840, 109.680
Angle α, β, γ (deg.)90.00, 92.99, 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, 2 molecules AB

#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.: 1
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.: 1
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, JR5.1 ... , 2 types, 2 molecules GH

#3: Protein T-CELL RECEPTOR, JR5.1 ALPHA CHAIN


Mass: 22567.066 Da / Num. of mol.: 1 / 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, JR5.1 BETA CHAIN


Mass: 27229.176 Da / Num. of mol.: 1 / Mutation: S184C, C202A
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, 235 molecules J

#5: Protein/peptide deamidated Gliadin-alpha2 peptide


Mass: 1380.500 Da / Num. of mol.: 1 / Mutation: Q5E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe authors state that there are mutations T174C in T-CELL RECEPTOR, JR5.1 ALPHA CHAIN, S184C and ...The authors state that there are mutations T174C in T-CELL RECEPTOR, JR5.1 ALPHA CHAIN, S184C and C202A in T-CELL RECEPTOR, JR5.1 BETA CHAIN, Q5E in deamidated Gliadin-alpha2 peptide.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 0.15 - 0.25M CaOAc, 0.1M Tris/HCl, 12-18% PEG3350, Additives:2-3 mM reduced and oxidised Glutathione
PH range: pH8.0-8.5

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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 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→60.47 Å / Num. obs: 32383 / % possible obs: 97.77 % / Redundancy: 1.9 % / Biso Wilson estimate: 58.53 Å2 / Rmerge(I) obs: 0.1061 / Net I/σ(I): 5.87

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.7→60.47 Å / Cor.coef. Fo:Fc: 0.9111 / Cor.coef. Fo:Fc free: 0.8495 / SU R Cruickshank DPI: 0.529 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.512 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1636 5.05 %RANDOM
Rwork0.1837 ---
obs0.1864 32383 97.77 %-
Displacement parametersBiso mean: 42.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.3022 Å20 Å2-2.1357 Å2
2---2.9853 Å20 Å2
3---3.2875 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: 1 / Resolution: 2.7→60.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 28 232 6624
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096562HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.148951HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2954SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes951HARMONIC5
X-RAY DIFFRACTIONt_it6562HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion865SEMIHARMONIC5
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_contact7079SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.282 119 4.57 %
Rwork0.2299 2486 -
all0.2322 2605 -
obs--97.77 %
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)
10.6521-0.0537-0.52941.0187-0.62032.04720.08530.18190.0395-0.0102-0.09830.04-0.2764-0.17780.013-0.08-0.001-0.0265-0.0177-0.0131-0.1095-20.49140.217152.4588
21.10560.1308-0.64420.48990.06053.2359-0.13270.1465-0.2588-0.0498-0.05790.05360.4131-0.01670.1907-0.08660.0022-0.0616-0.12610.0008-0.0609-15.619123.994549.4722
32.5446-0.0184-1.72181.5321-0.58414.40860.1189-0.3675-0.26110.21650.14530.1089-0.0475-0.2808-0.2643-0.1669-0.0729-0.0598-0.04940.1019-0.207-46.123216.6518102.1862
41.2211-0.344-0.44052.4077-0.40523.0810.004-0.44410.14890.24030.28670.1943-0.2971-0.3044-0.2906-0.19990.0022-0.046-0.0059-0.0133-0.2269-45.606736.9817103.3187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ G|* }
4X-RAY DIFFRACTION4{ H|* }

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