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- PDB-4pjg: Structure of human MR1-Ac-6-FP in complex with human MAIT B-F3-C1 TCR -

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Open data


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Basic information

Entry
Database: PDB / ID: 4pjg
TitleStructure of human MR1-Ac-6-FP in complex with human MAIT B-F3-C1 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 / 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-30W / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 1.3Dec 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_assembly / 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_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
Revision 1.4Nov 6, 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: 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)188,94510
Polymers188,4788
Non-polymers4662
Water14,106783
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)94,4725
Polymers94,2394
Non-polymers2331
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)94,4725
Polymers94,2394
Non-polymers2331
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.700, 70.980, 142.340
Angle α, β, γ (deg.)90.00, 103.93, 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: 22891.340 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: 27756.793 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 , 2 types, 785 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
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: 2.4→46.5 Å / Num. obs: 74265 / % possible obs: 89.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 40.65 Å2 / Net I/σ(I): 7.8

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.4→19.66 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9039 / SU R Cruickshank DPI: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 3702 4.99 %RANDOM
Rwork0.1672 ---
obs0.1694 74163 89.61 %-
Displacement parametersBiso mean: 35.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.8231 Å20 Å24.7561 Å2
2---3.8285 Å20 Å2
3---5.6516 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: 1 / Resolution: 2.4→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12336 0 32 783 13151
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112728HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217364HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4112SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes293HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1909HARMONIC5
X-RAY DIFFRACTIONt_it12728HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1644SEMIHARMONIC5
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_contact13975SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2488 266 4.88 %
Rwork0.2061 5185 -
all0.2082 5451 -
obs--89.61 %
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)
11.45410.2434-0.15731.2984-0.28811.34910.04670.14430.027-0.0257-0.07870.0699-0.01430.05080.032-0.0837-0.01450.0204-0.0379-0.0563-0.0267-73.293821.956526.5835
21.99230.6267-0.55322.0561-0.01211.50390.012-0.0524-0.08640.07550.02630.17930.1179-0.0593-0.0383-0.09110.00660.0329-0.12050.00590.0303-92.683235.243552.084
34.0472-0.66760.2852.3260.5431.8359-0.04920.42120.1113-0.19490.03570.3747-0.1263-0.230.0135-0.1406-0.0245-0.024-0.0840.01190.0078-99.713327.900831.6271
4-0.2837-1.28811.86713.05840.67861.12230.0842-0.0857-0.1337-0.1914-0.05330.04540.0617-0.0347-0.0309-0.07480.0629-0.0001-0.04580.00970.023319.536812.834956.9445
53.1944-1.23551.66413.0051-0.36252.76930.1226-0.0555-0.0904-0.20460.01270.05370.2350.0435-0.1354-0.10080.06590.0247-0.1267-0.0424-0.019712.783523.068155.0271
63.618-3.05062.97626.3233-3.05172.303-0.09860.42090.1781-0.4446-0.0083-0.17560.15390.43670.1069-0.08010.04080.0483-0.0464-0.0463-0.028217.255621.372447.1705
75.7674-3.01161.52851.5862-0.96861.0157-0.03430.1695-0.2673-0.03160.0252-0.0083-0.03030.00130.0092-0.03540.0611-0.00440.0647-0.04820.048516.037920.280158.5772
84.9375-1.06770.13511.65762.42322.7271-0.00930.67030.28610.1094-0.22550.26040.0616-0.08470.2348-0.11840.06010.01010.0221-0.01710.024143.66377.935969.3791
92.4229-0.2143-1.54861.10851.351512.5864-0.17010.0729-0.26310.2111-0.08070.0770.7595-0.62520.25080.00860.04980.0232-0.1606-0.01190.025636.53995.698480.1288
103.8247-0.5847-1.27514.1763-0.14834.2855-0.10490.3027-0.33840.3289-0.0651-0.16950.11140.14770.17-0.00360.01920.00950.0048-0.0660.108438.2455.658775.7376
110.9223-0.26230.89771.0097-1.00292.2341-0.1095-0.2540.06840.13740.02450.0874-0.2015-0.3280.0851-0.12090.06470.0115-0.017-0.0597-0.0655.608828.362574.868
124.3535-0.3996-1.5150.91860.54691.73060.03710.11960.0509-0.0276-0.0184-0.0986-0.0242-0.1168-0.0187-0.12590.0313-0.021-0.1511-0.0128-0.120432.456718.578285.3629
132.52970.1559-0.31233.16961.0723.2438-0.103-0.29070.26140.06220.18130.36910.042-0.3695-0.0783-0.25820.0498-0.03530.00550.03690.0174-16.049738.720151.0518
141.63710.0115-0.27932.1582-0.03891.3883-0.0582-0.09220.2345-0.13330.0694-0.2258-0.03530.1089-0.0112-0.19790.0163-0.0372-0.0623-0.01430.0239-1.361943.48447.1315
152.889-0.19542.35851.45710.03511.7298-0.14610.11210.3597-0.27490.01580.2144-0.068-0.05240.1303-0.1197-0.0449-0.06830.05260.09790.0436-27.118437.01928.3648
1610.7711-0.11071.44213.1835-0.00882.1154-0.4322-0.43410.96330.05510.20590.6213-0.3917-0.71060.2263-0.29590.1207-0.1037-0.0277-0.05440.1152-31.431551.815342.9587
17-0.07640.67681.86170-0.29632.5951-0.02680.04910.0231-0.1951-0.0129-0.1034-0.05490.41780.0397-0.0539-0.02180.04020.14750.0530.0847-35.692628.909617.976
184.42330.0796-2.42241.2776-0.24512.9010.0337-0.03260.26160.0213-0.0798-0.06540.17340.08180.0461-0.2079-0.02410.0042-0.08950.0217-0.1536-47.147724.477719.9272
195.17320.4993-1.46610.64390.653.8735-0.2111-0.137-0.20880.1369-0.08510.06420.34730.34090.2963-0.0477-0.00160.03810.0390.0508-0.054-40.75522.242323.3073
202.06112.841-0.19850-2.62360.5143-0.04780.17110.2747-0.1618-0.0260.2509-0.2586-0.14810.0738-0.05140.00840.02230.07690.01380.0589-56.064930.239117.1922
211.4612-2.5754-3.55343.41791.25614.9014-0.0440.093-0.1807-0.25850.0445-0.42070.03760.5515-0.0005-0.14-0.00230.06240.21170.04950.0279-22.417822.327811.9272
229.4035-0.70020.63512.99281.22743.6125-0.009-0.09370.3402-0.2659-0.0117-0.3266-0.08310.17480.0207-0.1681-0.01610.0836-0.01360.1120.015-16.159524.6921-1.647
233.7649-2.69310.689201.48555.8205-0.0684-0.05640.22190.00080.0697-0.0724-0.00330.055-0.00130.04570.02180.0249-0.02710.13070.0174-22.241623.52660.2487
245.42750.66181.26864.44120.29211.6584-0.11530.07320.3482-0.04030.2365-0.3023-0.03450.5745-0.1212-0.1962-0.06530.1244-0.00240.078-0.0172-13.794126.95860.0967
251.89440.1998-1.56572.2435-0.89724.0567-0.02450.29070.0704-0.2363-0.10260.0830.2505-0.25520.1272-0.0727-0.045-0.0164-0.0121-0.0036-0.1192-57.866323.40262.0828
263.33150.2967-2.303200.9040.6177-0.09060.14430.3834-0.48790.0986-0.1874-0.3144-0.075-0.0080.0105-0.0190.092-0.05510.058-0.117-44.223628.5869-13.9131
273.0182-2.23172.65324.5578-1.85283.1296-0.1252-0.001-0.14670.08050.174-0.26530.08020.3509-0.0488-0.09230.0420.1302-0.11750.0731-0.1054-25.768719.0844-7.1786
282.5115-1.39710.74973.78510.06533.438-0.00830.2709-0.3166-0.45660.29-0.06140.26560.2695-0.28180.03790.01380.1784-0.1413-0.0210.0494-33.065915.7348-17.2297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 171}
2X-RAY DIFFRACTION2{A|172 - 269}
3X-RAY DIFFRACTION3{B|0 - 98}
4X-RAY DIFFRACTION4{E|2 - 17}
5X-RAY DIFFRACTION5{E|18 - 52}
6X-RAY DIFFRACTION6{E|53 - 75}
7X-RAY DIFFRACTION7{E|76 - 108}
8X-RAY DIFFRACTION8{E|109 - 120}
9X-RAY DIFFRACTION9{E|121 - 150}
10X-RAY DIFFRACTION10{E|151 - 199}
11X-RAY DIFFRACTION11{F|3 - 123}
12X-RAY DIFFRACTION12{F|124 - 243}
13X-RAY DIFFRACTION13{C|1 - 55}
14X-RAY DIFFRACTION14{C|56 - 158}
15X-RAY DIFFRACTION15{C|159 - 269}
16X-RAY DIFFRACTION16{D|1 - 97}
17X-RAY DIFFRACTION17{G|2 - 17}
18X-RAY DIFFRACTION18{G|18 - 52}
19X-RAY DIFFRACTION19{G|53 - 91}
20X-RAY DIFFRACTION20{G|92 - 102}
21X-RAY DIFFRACTION21{G|103 - 116}
22X-RAY DIFFRACTION22{G|117 - 145}
23X-RAY DIFFRACTION23{G|146 - 165}
24X-RAY DIFFRACTION24{G|166 - 199}
25X-RAY DIFFRACTION25{H|3 - 108}
26X-RAY DIFFRACTION26{H|109 - 123}
27X-RAY DIFFRACTION27{H|124 - 201}
28X-RAY DIFFRACTION28{H|202 - 242}

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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