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- PDB-4pjf: Structure of human MR1-Ac-6-FP in complex with human MAIT B-C10 TCR -

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Basic information

Entry
Database: PDB / ID: 4pjf
TitleStructure of human MR1-Ac-6-FP in complex with human MAIT B-C10 TCR
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / Immune complex / Ac-6-FP
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 / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / 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-30W / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 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 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Refinement description
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 0 : statistics at the very beginning when nothing is done yet

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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: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: TCR-alpha
F: TCR-beta
G: TCR-alpha
H: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,98912
Polymers188,3388
Non-polymers6514
Water15,025834
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR-alpha
H: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5867
Polymers94,1694
Non-polymers4173
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: TCR-alpha
F: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4025
Polymers94,1694
Non-polymers2331
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.987, 71.698, 144.031
Angle α, β, γ (deg.)90.00, 104.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules ACBDEGFH

#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.: 2 / 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.: 2
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: 22891.295 Da / Num. of mol.: 2
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: 27686.791 Da / Num. of mol.: 2
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 , 3 types, 838 molecules

#5: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N5O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
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: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.45→69.6 Å / Num. obs: 79322 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.44 Å2 / Net I/σ(I): 12.7

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.45→35.87 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 3969 5.02 %RANDOM
Rwork0.1781 ---
obs0.1798 78987 98.99 %-
Displacement parametersBiso mean: 48.89 Å2
Baniso -1Baniso -2Baniso -3
1-3.8398 Å20 Å22.9713 Å2
2---8.7426 Å20 Å2
3---4.9029 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: 1 / Resolution: 2.45→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12331 0 44 834 13209
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00912726HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0817353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4109SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes298HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1903HARMONIC5
X-RAY DIFFRACTIONt_it12726HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion17.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1639SEMIHARMONIC5
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_contact13931SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2781 304 5.19 %
Rwork0.2219 5556 -
all0.2248 5860 -
obs--98.99 %
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)
11.20120.4188-0.3111.6904-0.22472.11040.03550.17570.0692-0.0065-0.05440.315-0.1925-0.10630.019-0.0755-0.00660.0204-0.0023-0.033-0.0254-6.239861.6531161.0819
22.13480.3715-0.37612.8489-0.38291.20240.0992-0.1025-0.16810.3035-0.187-0.00060.05570.16250.0878-0.0272-0.04010.0112-0.0277-0.023-0.14892.026455.0676171.5377
33.10691.1212-0.692.94090.61040.95030.0178-0.3323-0.14140.1332-0.0540.09910.1122-0.02470.0362-0.04520.04820.0122-0.05220.0016-0.0499-22.199371.1092191.7997
44.5228-1.3395-0.80393.06350.89981.79560.00180.59360.1639-0.3198-0.05030.4193-0.2168-0.38950.0485-0.12190.0101-0.0182-0.0282-0.0101-0.0651-29.033263.3331171.7164
51.54820.3-0.45741.7543-0.43351.71830.0131-0.25310.22850.05280.10430.17640.0143-0.2455-0.1174-0.13090.0578-0.03870.067-0.0056-0.0766-50.354240.098193.3372
62.19230.143-0.26543.18660.19020.8530.03440.08620.1711-0.16890.039-0.2434-0.04650.0055-0.0734-0.070.0116-0.0221-0.02650.0008-0.0832-37.862143.6742182.6943
72.4346-0.63531.9170.8514-0.0782.176-0.19170.07650.3856-0.1255-0.0052-0.0594-0.1035-0.1170.1969-0.078-0.0693-0.07290.04380.1014-0.0334-65.943139.1128167.1368
88.8097-0.25630.27661.6485-0.00812.3614-0.1533-0.29320.9967-0.05610.15120.5946-0.4278-0.62870.0021-0.24880.1524-0.0728-0.0353-0.00130.0155-69.074553.2067183.1553
90.6796-2.01822.01161.20310.58551.01890.08280.0521-0.0374-0.07990.07390.0724-0.03280.0983-0.15680.02040.03850.0055-0.0274-0.0154-0.0005-20.365812.896196.7519
104.0056-1.02840.69921.6312-0.74852.70650.0066-0.0023-0.2045-0.05620.09230.14570.11280.0677-0.0989-0.05490.0749-0.0289-0.1022-0.038-0.1414-25.969322.6421194.7086
112.0069-2.21343.12854.5675-2.47065.36050.03290.15670.0884-0.41740.0158-0.09690.0430.0112-0.04870.02090.05630.0408-0.015-0.0372-0.069-21.366521.3838187.1094
121.2852-1.49351.44161.1344-1.10420.6741-0.03040.1357-0.1611-0.02320.0550.0667-0.063-0.0093-0.02460.04140.06850.01070.1473-0.0866-0.0398-15.122717.1146201.2148
134.0157-1.3357-2.3730.15392.27425.2774-0.10.2531-0.46820.05260.0515-0.00840.6225-0.43680.04850.0615-0.0730.0353-0.1715-0.0435-0.0733-3.36625.7813219.2347
143.7683-0.008-1.49514.1551-1.09416.5345-0.19740.278-0.43810.07640.0672-0.02590.49140.03830.13020-0.06440.0608-0.0489-0.1192-0.06951.04996.5603214.6152
150.8889-0.77291.14951.0032-0.91511.8748-0.1242-0.27510.06670.05450.06520.0635-0.1796-0.36550.059-0.09270.09170.00020.1254-0.0429-0.1454-32.898528.3625214.3745
164.5873-0.4029-2.99820.58730.87823.00460.07620.4124-0.0306-0.0759-0.0141-0.1305-0.0938-0.2418-0.0622-0.04070.0506-0.0271-0.0238-0.0291-0.1215-6.182419.0248225.1392
172.5160.2767-0.12360.6979-0.24310.8680.0492-0.02450.0320.0569-0.0754-0.07690.05670.19390.0261-0.067-0.0311-0.0360.04730.0405-0.12527.740362.1488160.1816
187.78170.4542-1.41764.62730.04812.1656-0.013-0.13720.12430.0599-0.0364-0.212-0.02240.30930.0493-0.31280.0721-0.0203-0.0140.0645-0.032455.875760.6354142.3933
1910.2053.38420.464500.75626.4796-0.0962-0.27540.33160.21580.0719-0.03060.12520.08430.0243-0.04060.0367-0.0656-0.01630.08110.036649.021460.0806140.4073
204.59471.57531.35910.52672.49920.9237-0.07930.25950.43710.10030.2355-0.31180.09550.3435-0.1562-0.18570.0649-0.08410.03640.07690.215757.29264.3738139.0847
211.7383-0.0776-1.26520.6787-0.15531.5275-0.00080.19490.0217-0.1239-0.0385-0.04210.0804-0.07140.0393-0.0402-0.0241-0.0257-0.03560.0168-0.148815.069961.7765140.0799
225.3973-0.89253.03373.0008-0.85374.27630.29590.3794-0.6480.02920.043-0.2490.49690.554-0.3389-0.04580.08640.0479-0.1234-0.0374-0.138142.455555.3661129.5695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 84}
2X-RAY DIFFRACTION2{A|85 - 171}
3X-RAY DIFFRACTION3{A|172 - 269}
4X-RAY DIFFRACTION4{B|0 - 98}
5X-RAY DIFFRACTION5{C|1 - 83}
6X-RAY DIFFRACTION6{C|84 - 158}
7X-RAY DIFFRACTION7{C|159 - 269}
8X-RAY DIFFRACTION8{D|1 - 97}
9X-RAY DIFFRACTION9{E|1 - 17}
10X-RAY DIFFRACTION10{E|18 - 52}
11X-RAY DIFFRACTION11{E|53 - 75}
12X-RAY DIFFRACTION12{E|76 - 120}
13X-RAY DIFFRACTION13{E|121 - 156}
14X-RAY DIFFRACTION14{E|157 - 198}
15X-RAY DIFFRACTION15{F|3 - 123}
16X-RAY DIFFRACTION16{F|124 - 242}
17X-RAY DIFFRACTION17{G|1 - 108}
18X-RAY DIFFRACTION18{G|109 - 145}
19X-RAY DIFFRACTION19{G|146 - 165}
20X-RAY DIFFRACTION20{G|166 - 198}
21X-RAY DIFFRACTION21{H|3 - 123}
22X-RAY DIFFRACTION22{H|124 - 242}

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