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- PDB-6ovn: Crystal structure of the unliganded Clone 2 TCR -

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Basic information

Entry
Database: PDB / ID: 6ovn
TitleCrystal structure of the unliganded Clone 2 TCR
Components
  • Alpha chain Clone 2 TCR
  • Beta chain Clone 2 TCR
KeywordsIMMUNE SYSTEM / alpha beta / T-cell receptor / receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsShahine, A. / Rossjohn, J.
CitationJournal: J Immunol. / Year: 2019
Title: A TCR beta-Chain Motif Biases toward Recognition of Human CD1 Proteins.
Authors: Reinink, P. / Shahine, A. / Gras, S. / Cheng, T.Y. / Farquhar, R. / Lopez, K. / Suliman, S.A. / Reijneveld, J.F. / Le Nours, J. / Tan, L.L. / Leon, S.R. / Jimenez, J. / Calderon, R. / Lecca, ...Authors: Reinink, P. / Shahine, A. / Gras, S. / Cheng, T.Y. / Farquhar, R. / Lopez, K. / Suliman, S.A. / Reijneveld, J.F. / Le Nours, J. / Tan, L.L. / Leon, S.R. / Jimenez, J. / Calderon, R. / Lecca, L. / Murray, M.B. / Rossjohn, J. / Moody, D.B. / Van Rhijn, I.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha chain Clone 2 TCR
B: Beta chain Clone 2 TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5469
Polymers51,1402
Non-polymers4067
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Coelution as heterodimer via size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-65 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.188, 75.188, 109.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha chain Clone 2 TCR


Mass: 22865.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV (TCRA) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta chain Clone 2 TCR


Mass: 28274.836 Da / Num. of mol.: 1 / Mutation: C80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV (TCRB) / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 351 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→47.82 Å / Num. obs: 59111 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Rrim(I) all: 0.084 / Net I/σ(I): 18
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3375 / CC1/2: 0.74 / Rpim(I) all: 0.396 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G8F

4g8f


Resolution: 1.77→47.82 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.52
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 2924 4.95 %Random Selection
Rwork0.1699 ---
obs0.1714 59053 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 44.7254 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 1.77→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 22 344 3776
Biso mean--58.15 49.14 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.7990.28791890.265225912780100
1.799-1.830.25391390.251226962835100
1.83-1.86330.25421390.235426392778100
1.8633-1.89920.26731280.226126892817100
1.8992-1.93790.24291240.221226722796100
1.9379-1.98010.22691230.196327082831100
1.9801-2.02610.21431270.188127002827100
2.0261-2.07680.22291250.197226342759100
2.0768-2.13290.2271390.187426762815100
2.1329-2.19570.22641500.179726262776100
2.1957-2.26650.23371530.182726752828100
2.2665-2.34750.21321500.186826652815100
2.3475-2.44150.19971450.182426602805100
2.4415-2.55260.19351450.189826562801100
2.5526-2.68720.20331330.177226922825100
2.6872-2.85550.21171190.18126932812100
2.8555-3.07580.19911390.177226782817100
3.0758-3.38520.20431470.159926732820100
3.3852-3.87460.17761300.143427022832100
3.8746-4.87990.14641410.125726912832100
4.8799-37.60250.20821390.16752713285299
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)
10.0204-0.07620.04030.8052-0.17710.0983-0.0462-1.4106-0.33670.6578-0.3913-0.49770.10430.62850.0680.3784-0.2077-0.12821.58230.31570.265852.461677.65415.1216
23.38531.2444-2.27890.7005-0.91662.0228-0.0902-0.2082-0.2091-0.1035-0.1109-0.09580.16690.34990.16570.22480.05610.0040.18920.02010.218523.341569.06214.0457
36.68661.9331-0.86791.7956-0.3941.89360.10260.33870.2984-0.0716-0.08880.1246-0.1199-0.4685-0.00840.15790.0470.02810.45920.04070.241246.111185.289-7.9006
41.78420.3794-0.40730.74750.0981.6332-0.03710.2771-0.0493-0.02120.0299-0.086-0.02130.3053-0.01260.1180.02080.0240.23390.00350.18623.37879.24222.3374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 110 )A9 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 202 )A111 - 202
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 107 )B3 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 248 )B108 - 248

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