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- PDB-4nqc: Crystal structure of TCR-MR1 ternary complex and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 4nqc
TitleCrystal structure of TCR-MR1 ternary complex and covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / MR1 / T-Cell receptor / immune receptor complex / Ig-fold / protein binding / Schiff base / membrane
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 / alpha-beta T cell receptor complex / antigen processing and presentation of peptide antigen via MHC class I / 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 ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / antigen processing and presentation of peptide antigen via MHC class I / 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 / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2LJ / T cell receptor beta constant 1 / Beta-2-microglobulin / TRA@ protein / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: Nature / Year: 2014
Title: T-cell activation by transitory neo-antigens derived from distinct microbial pathways.
Authors: Corbett, A.J. / Eckle, S.B. / Birkinshaw, R.W. / Liu, L. / Patel, O. / Mahony, J. / Chen, Z. / Reantragoon, R. / Meehan, B. / Cao, H. / Williamson, N.A. / Strugnell, R.A. / Van Sinderen, D. ...Authors: Corbett, A.J. / Eckle, S.B. / Birkinshaw, R.W. / Liu, L. / Patel, O. / Mahony, J. / Chen, Z. / Reantragoon, R. / Meehan, B. / Cao, H. / Williamson, N.A. / Strugnell, R.A. / Van Sinderen, D. / Mak, J.Y. / Fairlie, D.P. / Kjer-Nielsen, L. / Rossjohn, J. / McCluskey, J.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Structure summary

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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: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,99711
Polymers187,3138
Non-polymers6843
Water18,7361040
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7903
Polymers43,4602
Non-polymers3301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-9 kcal/mol
Surface area17350 Å2
MethodPISA
2
C: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7903
Polymers43,4602
Non-polymers3301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area18110 Å2
MethodPISA
3
D: TCR alpha chain
E: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,1972
Polymers50,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25 kcal/mol
Surface area19090 Å2
MethodPISA
4
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2203
Polymers50,1972
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-37 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.760, 71.110, 144.280
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number5
Space group name H-MC121
Detailsheterodimer with beta microglobulin / heterodimer with TCR beta chain / heterodimer with TCR alpha chain / heterodimer with MR1

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Components

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Protein , 4 types, 8 molecules ACBFDGEH

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, Beta 2 microglobulin, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein TCR alpha chain


Mass: 22650.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR-alpha / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6P4G7*PLUS
#4: Protein TCR beta chain


Mass: 27546.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR-beta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01850*PLUS

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Non-polymers , 3 types, 1043 molecules

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


Mass: 330.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O7
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1040 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 293 K / pH: 6.3
Details: 12% (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→33.42 Å / Num. obs: 74555 / % possible obs: 100 % / Observed criterion σ(I): 7.8 / Biso Wilson estimate: 40.5 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33.42 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.892 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3757 5.04 %RANDOM
Rwork0.165 ---
obs0.168 74553 100 %-
Displacement parametersBiso mean: 29.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.1817 Å20 Å20.0896 Å2
2---8.2393 Å20 Å2
3---5.0575 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12382 0 45 1040 13467
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1617481HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4200SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1901HARMONIC5
X-RAY DIFFRACTIONt_it12828HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1647SEMIHARMONIC5
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_contact14657SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2923 281 5.15 %
Rwork0.2103 5180 -
all0.2145 5461 -
obs--100 %
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)
11.4131-0.33730.37461.024-0.05571.5514-0.00250.24020.22110.01010.0129-0.18360.11350.1598-0.0104-0.104-0.0443-0.02470.0162-0.00470.003848.194477.2281225.4665
23.1493-1.04180.64540.0021.5730.12070.0327-0.16420.13280.14750.0196-0.00810.01240.1434-0.0523-0.10360.0011-0.014-0.036-0.0478-0.029842.45880.9379235.9761
30.61140.3850.32530.93960.11290.69570.1281-0.11470.17410.0465-0.0050.10190.0731-0.056-0.1232-0.0487-0.010.0112-0.0032-0.0139-0.021139.759774.1724236.3441
44.36790.3581.20753.48013.0714.2923-0.1535-0.0550.49760.1830.0321-0.002-0.170.00120.1215-0.09160.0313-0.0856-0.0018-0.06140.004466.707980.5468253.3782
51.025-1.7138-0.74831.11190.05390.9933-0.0595-0.07670.14340.10470.0486-0.11830.0013-0.05510.011-0.05530.0458-0.08110.0711-0.1052-0.059767.889775.957262.2372
64.91120.34141.14022.206-0.47182.2038-0.07470.35270.50440.0732-0.0499-0.526-0.31270.64270.1246-0.2247-0.1297-0.05660.00060.01390.025967.38389.2066235.1816
70.81190.2936-0.173.17660.8241.8950.00320.09840.0198-0.0613-0.01780.1927-0.1425-0.01920.0146-0.04950.00250.0131-0.019-0.0192-0.0561-5.795962.8106161.8369
81.70420.1979-0.29792.1851-0.06031.2247-0.039-0.097-0.04850.0887-0.0830.01370.11460.11780.1221-0.0286-0.0202-0.0043-0.034-0.0142-0.08771.875855.6738171.8288
92.43380.7264-1.61070.6036-0.21212.03810.0451-0.2246-0.0585-0.0167-0.00530.20370.0045-0.0417-0.0398-0.01320.0330.0424-0.06850.00660.0325-22.514873.4728190.0198
101.74420.0178-0.39942.75820.3720.0507-0.0489-0.25790.0020.3721-0.03250.29760.1760.07910.0814-0.02320.0250.0598-0.03360.0158-0.0061-21.613570.6755193.9926
112.46690.6368-0.15280.7398-0.08622.2661-0.0069-0.01090.0557-0.0359-0.0106-0.10560.09570.22560.0175-0.09010.0079-0.0186-0.01450.0356-0.088928.558961.6993161.5011
124.5666-0.4378-2.45680.23430.11621.53060.00530.01020.09290.0613-0.018-0.29880.07070.29160.0127-0.11010.0183-0.00960.13430.0241-0.036238.014362.61150.0477
136.31980.59331.81141.70342.07762.9037-0.1785-0.03650.50690.01760.0848-0.23940.08590.28910.0937-0.24140.06670.00920.01460.07280.111153.457463.6451141.0767
141.73820.3967-1.07561.2331-1.00062.3338-0.09790.21310.0421-0.1593-0.08910.01450.1445-0.11820.1871-0.0348-0.0208-0.00850.02170.0041-0.076912.258761.7922141.3616
151.41840.193-1.37360.0027-0.88822.1409-0.00750.08370.0395-0.0732-0.096-0.065-0.13580.03270.10350.0295-0.00740.01840.0239-0.0061-0.0614.845461.3637144.4568
16-0.8169-1.91011.185401.90672.6574-0.03450.15720.1484-0.05890.11920.05960.03-0.0215-0.0848-0.07-0.01740.05020.00840.0787-0.077227.223467.4426125.5592
174.6964-1.26812.53122.8019-0.674.68110.25110.2597-0.3738-0.10020.0012-0.14940.57840.6015-0.2523-0.04610.11650.0478-0.14160.0035-0.182941.875156.2338129.9746
182.46640.52920.42623.02220.50261.9842-0.10860.48240.1505-0.1419-0.06930.4752-0.1828-0.40450.1778-0.10710.0022-0.0055-0.01610.0035-0.0665-28.889764.9295171.7054
193.02121.36151.36721.5240.94231.3927-0.0244-0.0052-0.07990.0040.06310.07360.09890.0043-0.0387-0.0306-0.04570.0173-0.03680.0537-0.054820.141257.4557224.4361
201.41991.3611.91320.8391.0241.0097-0.0287-0.1214-0.12540.0840.0226-0.05490.0147-0.08060.0061-0.0125-0.05360.01020.03950.02260.001812.55252.1185214.9809
213.13750.3457-1.12051.59290.55197.0965-0.0901-0.2116-0.3074-0.275-0.0607-0.00050.48370.34340.1508-0.0703-0.00880.031-0.16050.0721-0.0215-1.007542.5364200.7445
221.16090.48270.531.32011.20631.9696-0.05760.19060.0318-0.15280.0133-0.0028-0.10630.15780.0443-0.0577-0.0534-0.01710.04120.0546-0.063731.751967.174205.7171
230.36180.8677-0.76200.33950.6084-0.0122-0.0684-0.09390.0838-0.0381-0.12490.17890.14120.0503-0.0688-0.0004-0.02110.09150.0125-0.075624.369353.9282189.5304
245.5478-0.0221-2.19011.5136-0.23352.45420.0978-0.4085-0.1411-0.0536-0.0523-0.0461-0.04020.2073-0.0455-0.0249-0.0372-0.0055-0.06080.0184-0.1152.489453.2587196.5785
254.3065-0.0715-2.31820-0.42321.45810.03660.00880.094-0.08080.01260.0026-0.04450.1089-0.04930.0089-0.0326-0.0368-0.01780.04090.02437.433659.9907186.2972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|0 - A|84 }
2X-RAY DIFFRACTION2{ A|85 - A|114 }
3X-RAY DIFFRACTION3{ A|115 - A|182 }
4X-RAY DIFFRACTION4{ A|183 - A|244 }
5X-RAY DIFFRACTION5{ A|251 - A|269 }
6X-RAY DIFFRACTION6{ B|1 - B|96 }
7X-RAY DIFFRACTION7{ C|0 - C|84 }
8X-RAY DIFFRACTION8{ C|85 - C|171 }
9X-RAY DIFFRACTION9{ C|172 - C|216 }
10X-RAY DIFFRACTION10{ C|217 - C|269 }
11X-RAY DIFFRACTION11{ D|2 - D|83 }
12X-RAY DIFFRACTION12{ D|84 - D|135 }
13X-RAY DIFFRACTION13{ D|136 - D|198 }
14X-RAY DIFFRACTION14{ E|3 - E|73 }
15X-RAY DIFFRACTION15{ E|74 - E|109 }
16X-RAY DIFFRACTION16{ E|110 - E|124 }
17X-RAY DIFFRACTION17{ E|125 - E|239 }
18X-RAY DIFFRACTION18{ F|1 - F|97 }
19X-RAY DIFFRACTION19{ G|2 - G|91 }
20X-RAY DIFFRACTION20{ G|92 - G|120 }
21X-RAY DIFFRACTION21{ G|121 - G|199 }
22X-RAY DIFFRACTION22{ H|1 - H|109 }
23X-RAY DIFFRACTION23{ H|110 - H|124 }
24X-RAY DIFFRACTION24{ H|125 - H|202 }
25X-RAY DIFFRACTION25{ H|203 - H|243 }

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