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- PDB-5d7k: Structure of MR1-reactive MAV36 TCR -

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Basic information

Entry
Database: PDB / ID: 5d7k
TitleStructure of MR1-reactive MAV36 TCR
Components
  • MAV36 TCR Alpha Chain
  • MAV36 TCR Beta Chain
KeywordsIMMUNE SYSTEM / Receptor / Antigen
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKeller, A.N. / Rossjohn, J.
CitationJournal: Immunity / Year: 2016
Title: Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition.
Authors: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / ...Authors: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / Pellicci, D.G. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 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
D: MAV36 TCR Alpha Chain
E: MAV36 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8513
Polymers50,7552
Non-polymers961
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-41 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.439, 135.439, 64.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-465-

HOH

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Components

#1: Protein MAV36 TCR Alpha Chain


Mass: 22708.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein MAV36 TCR Beta Chain


Mass: 28046.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV/TRBC / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: BTP, PEG 3350, NaAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→67.72 Å / Num. obs: 53709 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.043 / Net I/σ(I): 13.8 / Num. measured all: 685664 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1 / Redundancy: 12.2 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.941.2862.34166934250.7530.383100
9.11-67.720.03735.766405460.9990.01199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Aimlessdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZB

4dzb


Resolution: 1.9→43.349 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 2684 5 %
Rwork0.1657 50987 -
obs0.1675 53671 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.72 Å2 / Biso mean: 28.3294 Å2 / Biso min: 9.34 Å2
Refinement stepCycle: final / Resolution: 1.9→43.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 10 514 3930
Biso mean--37.13 38.61 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083533
X-RAY DIFFRACTIONf_angle_d1.1274808
X-RAY DIFFRACTIONf_chiral_restr0.052538
X-RAY DIFFRACTIONf_plane_restr0.005624
X-RAY DIFFRACTIONf_dihedral_angle_d13.2811256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.93460.31221380.260426632801
1.9346-1.97180.2381090.222626852794
1.9718-2.0120.2481740.209526412815
2.012-2.05580.23461470.195126482795
2.0558-2.10360.21491530.182426312784
2.1036-2.15620.18051540.175626592813
2.1562-2.21450.20411560.1726442800
2.2145-2.27960.22471170.167726752792
2.2796-2.35320.18451350.169226712806
2.3532-2.43730.21151420.170726892831
2.4373-2.53490.24151130.178227002813
2.5349-2.65020.2281450.184526632808
2.6502-2.78990.22441270.17827092836
2.7899-2.96470.2081600.168326532813
2.9647-3.19350.19061380.161827142852
3.1935-3.51480.17341490.148826692818
3.5148-4.02310.16361230.138827312854
4.0231-5.06740.15471260.131227542880
5.0674-43.36030.22761780.171227882966
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)
11.5135-0.00650.00721.8613-0.62673.78940.0429-0.1773-0.09250.19470.016-0.08620.00170.3402-0.0530.1113-0.04820.00320.178-0.00390.138530.4559-69.37180.7725
23.9617-2.30924.21392.7644-3.41315.94510.32740.3537-0.0629-0.3871-0.23990.02340.34740.3115-0.10090.1095-0.02030.04630.2131-0.01050.150523.9874-60.1422-20.0398
33.09490.6501-0.70573.88260.08372.81590.06750.16910.3633-0.0360.0515-0.0581-0.29490.1698-0.08960.1033-0.0476-0.00330.24440.01870.17113.9683-48.3916-23.5012
45.5014-0.12760.14519.948-0.79534.2933-0.0011-0.118-0.8091-0.1427-0.06620.23240.6961-0.10920.05970.33660.0395-0.04750.28860.01610.27166.4014-57.56317.6186
51.8086-0.73730.15963.49690.63073.0054-0.1584-0.2153-0.28470.0902-0.06290.17190.0635-0.14590.17150.1392-0.01040.05860.16560.0340.1614.5544-62.356616.1318
62.4480.25771.6862.21771.09093.2888-0.441-0.21290.46290.43550.1483-0.1406-0.7793-0.27890.24020.28980.051-0.02220.1756-0.02730.16075.1954-43.53035.4384
70.8422-0.2446-0.26041.66911.12883.2724-0.05160.09070.05110.09770.0774-0.00810.00180.1125-0.03850.0673-0.0322-0.01110.16340.01710.12114.1465-53.5493-15.705
82.5090.34981.11832.94531.56665.053-0.1404-0.38290.32780.45-0.19270.3405-0.1042-0.59310.30810.13910.02240.03910.2481-0.03190.2078-4.9851-47.528-2.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 102 )D0
2X-RAY DIFFRACTION2chain 'D' and (resid 103 through 116 )D0
3X-RAY DIFFRACTION3chain 'D' and (resid 117 through 200 )D0
4X-RAY DIFFRACTION4chain 'E' and (resid 2 through 14 )E0
5X-RAY DIFFRACTION5chain 'E' and (resid 15 through 107 )E0
6X-RAY DIFFRACTION6chain 'E' and (resid 108 through 122 )E0
7X-RAY DIFFRACTION7chain 'E' and (resid 123 through 213 )E0
8X-RAY DIFFRACTION8chain 'E' and (resid 214 through 242 )E0

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