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- PDB-7ryl: T cell receptor CO3 -

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Basic information

Entry
Database: PDB / ID: 7ryl
TitleT cell receptor CO3
Components
  • T cell receptor delta variable 1,T cell receptor alpha chain constant
  • T cell receptor gamma variable 4,T cell receptor beta constant 1
KeywordsIMMUNE SYSTEM / CD1 / TCR / lipid antigen
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin complex / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin complex / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / innate immune response / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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 / Mainly Beta
Similarity search - Domain/homology
T cell receptor gamma variable 4 / T cell receptor delta variable 1 / T cell receptor alpha chain constant / T cell receptor beta constant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2022
Title: Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors.
Authors: Wegrecki, M. / Ocampo, T.A. / Gunasinghe, S.D. / von Borstel, A. / Tin, S.Y. / Reijneveld, J.F. / Cao, T.P. / Gully, B.S. / Le Nours, J. / Moody, D.B. / Van Rhijn, I. / Rossjohn, J.
History
DepositionAug 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T cell receptor gamma variable 4,T cell receptor beta constant 1
D: T cell receptor delta variable 1,T cell receptor alpha chain constant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8645
Polymers51,6102
Non-polymers2543
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-58 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.987, 76.414, 113.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein T cell receptor gamma variable 4,T cell receptor beta constant 1


Mass: 27987.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV4, TCRGV4, TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C4DH28, UniProt: P01850
#2: Protein T cell receptor delta variable 1,T cell receptor alpha chain constant


Mass: 23622.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV1, TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B0GX56, UniProt: P01848
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15M Ammonium sulfate, 15% PEG 4000, 0.1 MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.93222 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93222 Å / Relative weight: 1
ReflectionResolution: 2→45.47 Å / Num. obs: 30668 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.71 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.743 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2241 / CC1/2: 0.538

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6B

4x6b


Resolution: 2→45.47 Å / SU ML: 0.2383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1544 5.05 %
Rwork0.1986 29042 -
obs0.2011 30586 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.57 Å2
Refinement stepCycle: LAST / Resolution: 2→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 14 291 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333539
X-RAY DIFFRACTIONf_angle_d0.62864817
X-RAY DIFFRACTIONf_chiral_restr0.046521
X-RAY DIFFRACTIONf_plane_restr0.0045620
X-RAY DIFFRACTIONf_dihedral_angle_d13.12151251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.30881390.282575X-RAY DIFFRACTION99.78
2.06-2.140.29661390.26162617X-RAY DIFFRACTION99.71
2.14-2.220.30041510.24042566X-RAY DIFFRACTION99.89
2.22-2.330.36061290.23472625X-RAY DIFFRACTION100
2.33-2.450.30341460.22942592X-RAY DIFFRACTION99.93
2.45-2.60.2611440.22912616X-RAY DIFFRACTION99.93
2.6-2.80.27861350.21712624X-RAY DIFFRACTION99.96
2.8-3.080.2531430.20072634X-RAY DIFFRACTION100
3.08-3.530.23031430.18472662X-RAY DIFFRACTION99.96
3.53-4.450.20191380.16172691X-RAY DIFFRACTION100
4.45-45.470.22091370.1812840X-RAY DIFFRACTION99.97
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)
13.34813539101-2.287169110731.1678660382.84739212918-0.7825314855653.070084872710.08986098924160.31575025628-0.0364650664485-0.428310702723-0.166284279004-0.19649095183-0.0247550156180.2573344594450.06762861192910.263028118545-0.04444829447490.0674544740.211603285966-0.02498835415470.21292098391850.473581025332.141599345631.179615746
22.7962953859-0.731725107812-1.239680644332.242298889441.033935867024.879708407640.1299256123310.0450555730361-0.0887634524666-0.1984308268-0.1232261898710.03914099063950.0554612121477-0.0836091786958-0.01441696019710.157414114890.00115906445748-0.02385697255370.1739917283880.003920527978060.13372468009733.189378703156.573685888637.0620761888
36.23055045096-3.86087197139-1.497311967676.066284396663.263930840194.389235636760.01262544529610.0801016086166-0.650276920173-0.0689990087604-0.2636349853961.117634022880.312548239765-0.6820248488010.3577875436350.177715059231-0.1033231761550.04958628070350.3333211977470.06057522079280.31231292167335.763821668825.87904257750.6078576679
43.34271803898-0.8133346654610.7948500021295.711890177910.6127848450833.08931973814-0.0427986712648-0.245025258681-0.5068698677660.0805887889230.135277518801-0.1841326847640.10896035495-0.0712442555308-0.04114676839070.113009707822-0.00425973315170.03782883762270.2611696417270.04334160333190.24002780094745.358797901627.079850311552.3644388505
51.39111383447-0.81597132570.7240718168477.764254641861.146718590972.108511191220.018639371124-0.54808765621-0.4584438433380.2209111585730.0740260798422-0.01161667298280.0764260539208-0.0962907572851-0.1057400435710.1624676417170.005695120219150.0316785895630.3981400895870.1322551579580.34503487217745.501333109723.863402381460.6346457798
62.51593069245-1.86066822369-0.1951873861276.876372909631.19727923982.26315214818-0.253536313248-0.0963544965428-0.173685215730.3944783918420.112978141733-0.1965417675360.1081706945920.0581331894250.1603510362180.1661099635650.01297746554390.05618128233890.2466430148750.04439475079510.17577278876442.145555216633.67286076853.0321072299
73.88449809189-5.50047727463-0.09569678204998.161980824090.2508801865764.00089769849-0.1445664872740.316711850842-0.07219907345120.00633491561852-0.0143013955497-0.2808958273280.6352052641790.452721400456-0.00977494575770.2970433799740.0167883619970.0512613832430.1979634682120.02981356551040.24795315720551.182464462521.189953386844.3284653147
86.41209545172-5.3623890344-1.580703485335.501487822271.460835124930.445863507568-0.0681363304207-0.50032700180.1843527617170.2283628050460.403976314459-0.112144621254-0.550750300241-0.362541613846-0.09762825722020.4272409853580.1545980667960.143959045610.4411564227480.08808084038770.26216419394428.313155482145.130790385157.9532165081
96.900887151515.29582067947-4.611919307477.89143489695-5.086447819323.69630684074-0.04734658648991.060463485570.579620057914-0.3930549376670.7755302656050.780171855179-0.257471543357-1.13950728004-0.8499070861980.2826895929980.00605582772220.03436962150180.5108788624910.009255927375150.36565896081520.450440274460.21857921142.5427382707
108.428648058670.1663300384945.826180142747.965645311961.233004332884.368020802020.3888330192390.355496781153-1.15605499342-0.02039075799570.1000010805231.181674563021.255030225-0.912051364656-0.6019830253670.551778550611-0.1647394452140.03987154245890.585071673044-0.003897021740790.56027481766118.872015463845.242239484848.6474234723
117.474162869611.302668049083.888271257873.874830239462.043954016926.13167562301-0.0440141373739-0.0693621542889-0.3210094049190.1016458943810.0933292293396-0.1350480883540.282033974190.127637905496-0.02301200759740.160415678171-0.01223757030730.07260874346880.2878143916320.009996749794780.16215034151327.897440580451.952207702849.7232974467
122.38247378285-4.08367925939-2.105484174768.3624557864.628242982563.287932681240.6562648741980.845248028925-0.672539008537-0.6251581260070.3370127008441.70824102541-0.105148172269-2.92483723591-0.8826084593330.422305915883-0.0314742762014-0.03104024232021.35367791389-0.03127926887850.76041489090112.321268745952.566525361641.8311915654
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 8 through 127 )CA8 - 1271 - 118
22chain 'C' and (resid 128 through 248 )CA128 - 248119 - 239
33chain 'D' and (resid 2 through 15 )DC2 - 151 - 14
44chain 'D' and (resid 16 through 53 )DC16 - 5315 - 52
55chain 'D' and (resid 54 through 79 )DC54 - 7953 - 78
66chain 'D' and (resid 80 through 96 )DC80 - 9679 - 95
77chain 'D' and (resid 97 through 108 )DC97 - 10896 - 107
88chain 'D' and (resid 109 through 122 )DC109 - 122108 - 121
99chain 'D' and (resid 123 through 141 )DC123 - 141122 - 140
1010chain 'D' and (resid 142 through 156 )DC142 - 156141 - 155
1111chain 'D' and (resid 157 through 181 )DC157 - 181156 - 180
1212chain 'D' and (resid 182 through 194 )DC182 - 194181 - 193

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