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- PDB-4pje: Structure of human MR1-Ac-6-FP in complex with human MAIT B-B10 TCR -

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Basic information

Entry
Database: PDB / ID: 4pje
TitleStructure of human MR1-Ac-6-FP in complex with human MAIT B-B10 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 / ACETATE ION / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 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_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_conn.pdbx_dist_value / _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
Revision 1.4Nov 13, 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)189,75926
Polymers188,2268
Non-polymers1,53318
Water26,3561463
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
E: TCR-alpha
F: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,17017
Polymers94,1134
Non-polymers1,05713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
G: TCR-alpha
H: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5899
Polymers94,1134
Non-polymers4765
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.040, 72.460, 143.360
Angle α, β, γ (deg.)90.00, 104.50, 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: 22879.352 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: 27642.717 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 , 6 types, 1481 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: 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
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1463 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
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: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.95→46.9 Å / Num. obs: 155088 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.88 Å2 / Net I/σ(I): 11

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9427 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 7803 5.03 %RANDOM
Rwork0.171 ---
obs0.1724 155058 97.75 %-
Displacement parametersBiso mean: 37.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.6763 Å20 Å20.5217 Å2
2---7.7037 Å20 Å2
3---4.0274 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: 1 / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12651 0 1560 1463 15674
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0317825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4362SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes341HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1933HARMONIC5
X-RAY DIFFRACTIONt_it13101HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1650SEMIHARMONIC5
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_contact15676SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2161 575 5.05 %
Rwork0.1947 10812 -
all0.1958 11387 -
obs--97.75 %
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)
10.796-0.3011-0.30331.2230.27230.89970.03910.1310.0663-0.0345-0.03560.1291-0.0697-0.0211-0.0035-0.0272-0.0039-0.0009-0.0045-0.0029-0.0587-78.372220.178821.7015
21.1774-0.0303-0.28372.537-0.56180.56610.0357-0.0327-0.08480.2246-0.113-0.15530.0210.08370.0772-0.008-0.0160.0008-0.0046-0.0101-0.0959-70.56612.889432.18
31.48580.5108-0.6321.5734-0.0220.97490.0255-0.2211-0.090.0728-0.0520.13260.0674-0.00130.0264-0.03130.01630.0416-0.0420.0107-0.0209-94.293829.088352.6233
41.42420.36820.02960.65940.73911.44040.0630.15230.1214-0.085-0.18790.2532-0.1029-0.20580.1249-0.0323-0.00570.0151-0.0634-0.00470.0494-100.425721.872437.5464
52.6783-1.0355-0.45832.23270.54430.5404-0.00890.5260.1687-0.2952-0.07580.2752-0.1446-0.08850.0847-0.02640.0205-0.0381-0.01580.01820.0011-100.462122.235728.663
66.0257-2.6179-0.72163.80070.48181.6901-0.10510.13350.2387-0.13080.05890.3566-0.2478-0.2720.0461-0.03870.0141-0.0239-0.0521-0.007-0.0205-99.733124.079333.0227
72.8344-0.1951-0.04422.09540.28450.9781-0.03060.1307-0.0703-0.2237-0.06770.49610.0059-0.24320.0983-0.0805-0.0144-0.0228-0.0452-0.03630.0532-106.483616.49633.2953
81.9146-0.45340.06541.3243-0.24951.2836-0.0823-0.35060.16720.07480.16630.06940.013-0.1835-0.084-0.08770.054-0.02230.0421-0.0281-0.0579-12.977734.005954.0467
92.00060.4429-0.0522.06350.04010.87020.0435-0.0050.2357-0.2861-0.0835-0.1697-0.04320.02880.04-0.05510.02070.0095-0.05480.0076-0.0308-0.661637.180743.1691
102.1684-0.57941.93780.1578-0.20612.049-0.14370.09690.2472-0.04890.00210.0091-0.1358-0.05070.1416-0.0434-0.0359-0.08890.01930.09210.001-28.476832.310328.3514
110.2403-3.7877-0.54981.9225-0.36722.0015-0.02740.10930.1688-0.26410.04890.2803-0.1113-0.5234-0.0215-0.11780.1108-0.07550.00720.0360.0238-31.923745.492139.0374
125.92420.2241.25941.576-0.14741.1926-0.0801-0.74750.7651-0.03440.00520.4522-0.1994-0.4910.0749-0.22250.0984-0.0361-0.0058-0.08070.0121-29.667145.300746.9367
135.5101-1.2921-1.612.6078-0.00811.1452-0.0697-0.190.4607-0.05660.01780.6992-0.2473-0.64440.0519-0.17040.1355-0.09690.1646-0.08350.1484-37.214546.015444.6179
140.5984-0.03490.70030.9344-1.39622.04980.031-0.03230.2505-0.15420.1553-0.0401-0.1598-0.1483-0.1863-0.12020.1952-0.1552-0.1566-0.09110.3101-30.326855.101642.838
151.90510.2488-0.14740.6168-0.06461.3808-0.0122-0.0285-0.02260.0271-0.0161-0.06330.08270.17130.0284-0.07360.0109-0.0143-0.00120.0482-0.0719-42.858919.714120.2395
168.6183-0.09670.95692.5571-0.19943.9932-0.1492-0.28851.04250.01630.103-0.3696-0.25060.50570.0462-0.13760.02240.0025-0.0346-0.02780.2284-18.041621.66490.0877
171.88250.1954-0.56891.1665-0.6871.5682-0.0240.1202-0.0151-0.0904-0.0136-0.01550.1113-0.08020.0377-0.038-0.02840.0023-0.05240.0181-0.1128-59.844320.08450.422
181.39590.0707-0.87570.00550.29171.0848-0.0380.13290.0152-0.12550.0544-0.01750.1998-0.128-0.0164-0.0165-0.01530.0096-0.0170.0259-0.0503-51.223420.4161-2.1699
194.5899-1.15481.71941.5564-0.81241.93770.15060.1213-0.7572-0.00110.0683-0.06850.22330.3047-0.2189-0.10560.07760.0259-0.1072-0.0258-0.0384-27.151713.1043-6.9833
203.6242-2.05790.44445.57530.77964.24680.0140.3562-0.4204-0.3370.2565-0.14730.18980.1362-0.2706-0.05540.00910.0425-0.0682-0.0946-0.0905-38.509114.5997-19.3441
212.3561-0.48750.36581.4494-0.22970.8438-0.00940.06670.0824-0.06590.0341-0.0037-0.03340.0289-0.0247-0.02310.02260.0076-0.0005-0.0053-0.056115.04313.975453.7306
224.3923-1.77692.60350.83-0.94651.48930.01340.2434-0.0184-0.0262-0.01910.03740.0650.07450.0056-0.01020.03110.01250.0174-0.018-0.056923.32959.069963.206
232.3571-0.1288-0.10241.23130.30863.1043-0.00220.1539-0.27380.1697-0.01170.01390.49550.02830.01390.045600.0187-0.0788-0.0471-0.063636.807-0.13677.383
242.1595-0.53270.2762.0104-0.93622.2594-0.1054-0.34630.07630.0130.0208-0.0174-0.147-0.18320.0847-0.06920.05-0.0090.0741-0.0342-0.11633.325822.296773.6355
251.5628-0.63381.05481.4255-1.52541.9739-0.0827-0.37020.18660.13630.04180.0336-0.2329-0.20180.0409-0.02930.0498-0.00660.0769-0.0566-0.04443.382424.306472.4524
260.0243-0.72071.20460-0.01763.10370.07630.07060.06310.02150.06080.14990.1172-0.5721-0.1371-0.1091-0.0286-0.00330.08280.0123-0.126211.635410.361589.3046
273.2536-0.4462-0.62010.94810.38212.1143-0.06410.1541-0.1083-0.044-0.0070.00690.0892-0.14080.0711-0.10460.0006-0.0134-0.0809-0.0414-0.156731.15999.645682.5191
280.74220.5098-0.46780.1824-0.31611.25210.07320.06630.1002-0.0041-0.011-0.0595-0.1344-0.1484-0.06220.03910.0182-0.01880.0534-0.04310.016830.825915.657488.9075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 83}
2X-RAY DIFFRACTION2{A|84 - 171}
3X-RAY DIFFRACTION3{A|172 - 269}
4X-RAY DIFFRACTION4{B|0 - 19}
5X-RAY DIFFRACTION5{B|20 - 56}
6X-RAY DIFFRACTION6{B|57 - 77}
7X-RAY DIFFRACTION7{B|78 - 98}
8X-RAY DIFFRACTION8{C|1 - 84}
9X-RAY DIFFRACTION9{C|85 - 158}
10X-RAY DIFFRACTION10{C|159 - 269}
11X-RAY DIFFRACTION11{D|0 - 19}
12X-RAY DIFFRACTION12{D|20 - 61}
13X-RAY DIFFRACTION13{D|62 - 83}
14X-RAY DIFFRACTION14{D|84 - 96}
15X-RAY DIFFRACTION15{E|2 - 116}
16X-RAY DIFFRACTION16{E|117 - 198}
17X-RAY DIFFRACTION17{F|3 - 86}
18X-RAY DIFFRACTION18{F|87 - 122}
19X-RAY DIFFRACTION19{F|123 - 213}
20X-RAY DIFFRACTION20{F|214 - 242}
21X-RAY DIFFRACTION21{G|2 - 91}
22X-RAY DIFFRACTION22{G|92 - 120}
23X-RAY DIFFRACTION23{G|121 - 198}
24X-RAY DIFFRACTION24{H|3 - 63}
25X-RAY DIFFRACTION25{H|64 - 107}
26X-RAY DIFFRACTION26{H|108 - 122}
27X-RAY DIFFRACTION27{H|123 - 186}
28X-RAY DIFFRACTION28{H|187 - 242}

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