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- PDB-6ovo: Crystal structure of the unliganded PG10 TCR -

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Basic information

Entry
Database: PDB / ID: 6ovo
TitleCrystal structure of the unliganded PG10 TCR
Components
  • Alpha Chain T-Cell Receptor PG10
  • Beta Chain T-Cell Receptor PG10
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: 2.49 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
Revision 1.3Nov 13, 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: Alpha Chain T-Cell Receptor PG10
B: Beta Chain T-Cell Receptor PG10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2708
Polymers50,8492
Non-polymers4216
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Eluted at expected volume via size exclusion
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-69 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.620, 149.620, 55.991
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha Chain T-Cell Receptor PG10


Mass: 22873.312 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 T-Cell Receptor PG10


Mass: 27975.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV (TCRB) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 121 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.03 % / Description: Rod morphology
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium Sulfate

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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: Sep 29, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→74.81 Å / Num. obs: 25252 / % possible obs: 99.6 % / Redundancy: 10.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.048 / Net I/σ(I): 11.2
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2502 / CC1/2: 0.537 / Rpim(I) all: 0.402 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WJO

5wjo


Resolution: 2.49→44.826 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2216 1275 5.05 %
Rwork0.1767 --
obs0.179 25245 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.94 Å2 / Biso mean: 58.7487 Å2 / Biso min: 22.23 Å2
Refinement stepCycle: final / Resolution: 2.49→44.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 21 115 3604
Biso mean--105.72 53.79 -
Num. residues----447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4902-2.58990.32431470.27542626277399
2.5899-2.70770.3171430.278326512794100
2.7077-2.85050.27911340.240726382772100
2.8505-3.0290.28011260.219526592785100
3.029-3.26280.26021580.205326512809100
3.2628-3.59110.28541450.185326402785100
3.5911-4.11040.21241360.171326812817100
4.1104-5.17740.15181580.123326872845100
5.1774-44.83340.17671280.14672737286599
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)
16.6481-0.23170.46525.4376-1.50553.72350.2078-0.2206-0.18150.1106-0.02040.1202-0.1820.0143-0.14470.272-0.12310.0060.324-0.02270.236132.8501-54.56594.9281
26.09960.80261.76671.2591-0.94851.9117-0.32110.16680.8593-0.10530.15460.3626-0.3897-0.32130.14470.4480.1008-0.01130.541-0.01860.47542.8723-51.6160.7166
35.5773-0.16661.51884.7792-0.35792.42920.07880.2268-0.0632-0.26970.03680.03180.2774-0.113-0.10290.2743-0.1172-0.00450.35820.01550.248125.8007-76.556910.9132
42.1548-0.62961.38943.9101-2.14884.7945-0.03310.0617-0.02520.133-0.00850.1824-0.2749-0.36250.0420.1954-0.0017-0.00490.61870.00010.384-0.1307-66.07521.7348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 111 )A1 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 202 )A112 - 202
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 125 )B3 - 125
4X-RAY DIFFRACTION4chain 'B' and (resid 126 through 247 )B126 - 247

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