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- PDB-4ozg: D2 protein complex -

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Basic information

Entry
Database: PDB / ID: 4ozg
TitleD2 protein complex
Components
  • (HLA class II histocompatibility antigen, DQ ...) x 2
  • (T-cell receptor, d2, ...) 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / complement activation, classical pathway / trans-Golgi network membrane / antigen binding / lumenal side of endoplasmic reticulum membrane / 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 / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / endosome membrane / immune response / lysosomal membrane / Golgi membrane / extracellular exosome / 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) / MHC class II, beta chain, N-terminal ...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: 3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.type / _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_asym.entity_id / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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

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, d2, alpha chain
F: T-cell receptor, d2, beta chain
G: T-cell receptor, d2, alpha chain
H: T-cell receptor, d2, beta chain
I: deamidated Gliadin-alpha2 peptide
J: deamidated Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,85914
Polymers193,74910
Non-polymers1,1104
Water21612
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, d2, alpha chain
H: T-cell receptor, d2, beta chain
J: deamidated Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2996
Polymers96,8755
Non-polymers4241
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, d2, alpha chain
F: T-cell receptor, d2, beta chain
I: deamidated Gliadin-alpha2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5608
Polymers96,8755
Non-polymers6863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)266.024, 60.266, 138.235
Angle α, β, γ (deg.)90.00, 114.04, 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, d2, ... , 2 types, 4 molecules EGFH

#3: Protein T-cell receptor, d2, alpha chain /


Mass: 22463.986 Da / Num. of mol.: 2 / Mutation: T176C
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, d2, beta chain /


Mass: 27151.061 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 , 1 types, 2 molecules IJ

#5: Protein/peptide deamidated Gliadin-alpha2 peptide


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

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Sugars , 2 types, 3 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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, 13 molecules

#8: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe author state that there are mutations T176C in T-cell receptor, d2, alpha chain, C202A and ...The author state that there are mutations T176C in T-cell receptor, d2, alpha chain, C202A and S184C in T-cell receptor, d2, 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: 2.61 Å3/Da / Density % sol: 52.9 %
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: 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 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→43.48 Å / Num. obs: 39276 / % possible obs: 96.48 % / Redundancy: 1.9 % / Biso Wilson estimate: 80.28 Å2 / Rmerge(I) obs: 0.07389 / Net I/σ(I): 8.1

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 3→43.48 Å / Cor.coef. Fo:Fc: 0.8943 / Cor.coef. Fo:Fc free: 0.8567 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.401
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1958 4.99 %RANDOM
Rwork0.2026 ---
obs0.2045 39276 96.47 %-
Displacement parametersBiso mean: 80.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.066 Å20 Å22.7686 Å2
2---17.7091 Å20 Å2
3---12.6432 Å2
Refine analyzeLuzzati coordinate error obs: 0.459 Å
Refinement stepCycle: 1 / Resolution: 3→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12632 0 71 12 12715
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0517812HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5844SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes324HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1898HARMONIC5
X-RAY DIFFRACTIONt_it13046HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion3.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1734SEMIHARMONIC5
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_contact13658SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2645 136 4.68 %
Rwork0.2369 2769 -
all0.2382 2905 -
obs--96.47 %
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)
11.6981-1.1717-0.9052.40381.46183.5804-0.11490.2977-0.63990.1774-0.34050.13770.949-0.8010.4555-0.3442-0.29250.0499-0.2253-0.2122-0.2061191.957-10.6709136.3246
21.82040.2806-1.19411.39360.855.5102-0.05530.344-0.0082-0.1116-0.0785-0.0844-0.0431-0.8850.1338-0.5928-0.077-0.0284-0.1789-0.0964-0.3852190.6753.6937127.0696
31.5433-0.45190.54330.3315-0.65554.31030.10620.1938-0.4452-0.2664-0.36610.0337-0.0126-0.39860.26-0.2077-0.0176-0.17210.1026-0.2642-0.2006232.285335.3456192.2061
41.0771-0.20890.76650.1380.57874.01110.2104-0.06-0.604-0.0978-0.11130.27060.2789-0.4306-0.0991-0.2265-0.2093-0.22590.0104-0.08630.249234.188114.6088191.7452
50.6906-0.3178-0.01870.4573-0.3463.7144-0.1681-0.5455-0.14250.10.00960.28910.3393-0.31210.1585-0.2735-0.20960.1460.35190.02690.0761234.758919.599249.3818
61.0403-0.3786-0.41920.48070.62272.7618-0.2946-0.854-0.12760.14070.0573-0.0752-0.04340.38890.2374-0.1101-0.0336-0.21060.63460.13470.0524239.550236.2106250.389
71.31470.82321.17011.60611.36426.97960.06340.21930.07870.22390.0888-0.3344-0.44930.2275-0.1523-0.208-0.039-0.1144-0.6037-0.0173-0.1442200.744829.8167178.5962
81.33690.1992-0.28991.45311.53514.4397-0.0712-0.0873-0.0470.207-0.00920.02180.197-0.44850.0804-0.241-0.114-0.0356-0.526-0.034-0.3281195.236312.5845187.9433
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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