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- PDB-4pj9: Structure of human MR1-5-OP-RU in complex with human MAIT TRAJ20 TCR -

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Basic information

Entry
Database: PDB / ID: 4pj9
TitleStructure of human MR1-5-OP-RU in complex with human MAIT TRAJ20 TCR
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / Immune complex / 5-OP-RU
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2014
Title: A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells.
Authors: Eckle, S.B. / Birkinshaw, R.W. / Kostenko, L. / Corbett, A.J. / McWilliam, H.E. / Reantragoon, R. / Chen, Z. / Gherardin, N.A. / Beddoe, T. / Liu, L. / Patel, O. / Meehan, B. / Fairlie, D.P. ...Authors: Eckle, S.B. / Birkinshaw, R.W. / Kostenko, L. / Corbett, A.J. / McWilliam, H.E. / Reantragoon, R. / Chen, Z. / Gherardin, N.A. / Beddoe, T. / Liu, L. / Patel, O. / Meehan, B. / Fairlie, D.P. / Villadangos, J.A. / Godfrey, D.I. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: TCR-alpha
D: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5418
Polymers93,0184
Non-polymers5234
Water14,322795
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.560, 111.560, 204.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 1 / Fragment: UNP residues 23-292 / Mutation: C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TCR-alpha


Mass: 22517.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TCR-beta


Mass: 26908.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 799 molecules

#5: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-tris propane, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 89271 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 26.58 Å2 / Net I/σ(I): 9.6

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2→38.73 Å / Cor.coef. Fo:Fc: 0.9497 / Cor.coef. Fo:Fc free: 0.9348 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 4453 5.02 %RANDOM
Rwork0.1724 ---
obs0.1738 88733 99.95 %-
Displacement parametersBiso mean: 38.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.3855 Å20 Å20 Å2
2--0.3855 Å20 Å2
3----0.7711 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: 1 / Resolution: 2→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 35 795 7057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg18781HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2871SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes962HARMONIC5
X-RAY DIFFRACTIONt_it6441HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion2.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion830SEMIHARMONIC5
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_contact7593SEMIHARMONIC4
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2377 315 4.89 %
Rwork0.1997 6124 -
all0.2015 6439 -
obs--99.95 %
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)
12.0074-0.1014-0.2421.05680.00051.08930.0374-0.0062-0.31710.0741-0.00850.00240.22130.01-0.0288-0.0007-0.00670.0161-0.0715-0.0267-0.00037.88862.988423.8794
21.61430.13330.2961.3448-0.14461.66520.0740.20530.0077-0.1172-0.02960.1003-0.0367-0.0952-0.0444-0.06180.02760.0325-0.0666-0.0265-0.06613.229113.186715.854
300.4946-0.26480.65210.87081.2558-0.0405-0.02290.095-0.08590.0965-0.0691-0.1437-0.0331-0.056-0.1011-0.0130.0386-0.1095-0.003-0.102113.728715.221519.254
42.8512-0.8539-0.88361.79310.73462.45210.1670.4914-0.1458-0.3041-0.22720.06270.0678-0.22570.06020.09830.0965-0.02250.0167-0.04790.02829.806-11.99133.7492
53.4977-2.18532.82211.8763-3.17643.08990.13380.2873-0.47350.1736-0.05220.14330.13080.0403-0.0816-0.11730.0263-0.0347-0.069-0.1196-0.04567.0034-8.79275.702
62.5624-1.3479-4.1382.5473-1.48531.88860.0869-0.2242-0.60520.1478-0.0631-0.06450.21490.3157-0.02380.09060.0891-0.1584-0.0761-0.08890.174622.0326-25.095516.4361
74.004-3.01392.06412.7714-1.46462.85440.2260.0302-0.78770.19230.06030.5890.2662-0.163-0.2863-0.1515-0.0271-0.0249-0.2261-0.06670.02886.5689-13.98313.0068
82.81491.62441.67142.3901-0.70860.37720.1178-0.5625-0.74970.14680.13770.56830.1917-0.2716-0.25550.1062-0.04340.0512-0.12510.02540.44533.3914-22.331118.1495
92.3811-0.2983-0.27625.28521.83762.31310.00480.006-0.09930.10560.02670.14850.148-0.1518-0.0315-0.12260.0190.017-0.1361-0.0578-0.12417.14740.274313.5841
101.7941-0.6637-0.31090.44641.40321.51990.0872-0.1149-0.59070.40990.02540.26880.3987-0.0879-0.1125-0.0839-0.0285-0.0172-0.1539-0.00790.04119.9833-14.789517.2063
111.367-0.27091.03482.0140.15290.04730.03080.196-0.01080.0053-0.03160.043-0.0033-0.02410.00080.25640.0798-0.2581-0.1675-0.20170.611613.3591-32.114511.6457
120.0001-1.44060.26979.58840.38521.32510.12470.1969-0.7621-0.12510.22720.35510.2492-0.1257-0.3518-0.1383-0.041-0.1183-0.1019-0.1090.2843-0.025-15.90076.4722
130.0101-0.9201-0.78743.22510.10076.398-0.03130.2021-0.0562-0.26650.05180.19030.34150.0607-0.0205-0.14060.0524-0.1521-0.2184-0.2150.13229.9223-22.03865.5616
140.88720.96080.34352.6639-1.33063.57560.0809-0.06190.23170.0966-0.1305-0.0566-0.0889-0.05340.0496-0.0073-0.02370.0283-0.040.00940.051213.817243.381539.1288
150.66130.14970.18322.24620.18631.32560.01720.03670.10420.044-0.051-0.0135-0.0582-0.09840.0338-0.149-0.0270.0349-0.1774-0.006-0.11189.370834.825831.9886
162.4004-3.0589-0.64578.95321.11123.66930.12940.24630.1601-0.4333-0.1307-0.2121-0.28280.03390.0012-0.1059-0.04410.0458-0.12580.0181-0.045215.287739.290726.8588
170.86380.30480.19538.7896-0.35162.63770.10370.17920.1314-0.0805-0.3662-0.0749-0.1606-0.16760.2625-0.0598-0.00050.0268-0.04380.00360.05937.061744.309633.4292
180.6860.4506-0.24184.35881.17821.31110.1497-0.02050.31370.1831-0.1441-0.0069-0.1896-0.0429-0.00560.0339-0.00240.0453-0.0442-0.02860.08928.652344.73638.6896
190.7826-3.7662-0.77475.27551.45561.7515-0.0253-0.16070.3080.5217-0.08140.2036-0.3452-0.08170.10670.2044-0.00430.1857-0.1534-0.27460.0692-4.406466.624657.1449
204.12954.61221.29231.7094-2.51663.99690.0954-0.00980.19710.1420.0666-0.21080.06510.3661-0.16190.03670.00650.0301-0.1578-0.24070.02479.539461.078850.0654
214.29941.9586-3.39624.72261.56894.96890.1498-0.2010.34950.2589-0.2684-0.38010.0749-0.02340.11860.00030.00490.0693-0.1354-0.1350.05170.535858.682450.7047
224.6685-0.50481.23385.45190.07878.6780.2187-0.42370.96480.5708-0.2773-0.2104-0.37620.03740.05860.1383-0.05540.0727-0.1435-0.23330.1285.547165.754854.5478
231.55380.2863-0.192.46060.11382.45670.06280.0228-0.00610.2425-0.1230.1936-0.0003-0.1820.0602-0.1272-0.04630.0661-0.0594-0.0431-0.1194-6.406825.543941.0312
242.5833-0.4223-2.59063.39811.044500.0653-0.58630.21760.9348-0.0970.23990.2882-0.01460.03170.1579-0.04740.18530.0477-0.1579-0.1209-11.244236.471159.3694
253.27411.7353-1.61745.6377-0.9822.77840.33760.10580.63880.6084-0.14690.7601-0.3664-0.3549-0.1908-0.08040.10390.1828-0.1705-0.15750.0072-11.180856.429951.9643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|0 - 55}
2X-RAY DIFFRACTION2{A|56 - 133}
3X-RAY DIFFRACTION3{A|134 - 182}
4X-RAY DIFFRACTION4{A|183 - 270}
5X-RAY DIFFRACTION5{B|0 - 11}
6X-RAY DIFFRACTION6{B|12 - 19}
7X-RAY DIFFRACTION7{B|20 - 41}
8X-RAY DIFFRACTION8{B|42 - 51}
9X-RAY DIFFRACTION9{B|52 - 61}
10X-RAY DIFFRACTION10{B|62 - 71}
11X-RAY DIFFRACTION11{B|72 - 77}
12X-RAY DIFFRACTION12{B|78 - 90}
13X-RAY DIFFRACTION13{B|91 - 97}
14X-RAY DIFFRACTION14{C|2 - 17}
15X-RAY DIFFRACTION15{C|18 - 52}
16X-RAY DIFFRACTION16{C|53 - 75}
17X-RAY DIFFRACTION17{C|76 - 91}
18X-RAY DIFFRACTION18{C|92 - 116}
19X-RAY DIFFRACTION19{C|117 - 135}
20X-RAY DIFFRACTION20{C|136 - 145}
21X-RAY DIFFRACTION21{C|146 - 164}
22X-RAY DIFFRACTION22{C|165 - 198}
23X-RAY DIFFRACTION23{D|2 - 107}
24X-RAY DIFFRACTION24{D|108 - 122}
25X-RAY DIFFRACTION25{D|123 - 239}

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