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- PDB-4wnq: THE MOLECULAR BASES OF DELTA/ALPHA-BETA T-CELL MEDIATED ANTIGEN R... -

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Basic information

Entry
Database: PDB / ID: 4wnq
TitleTHE MOLECULAR BASES OF DELTA/ALPHA-BETA T-CELL MEDIATED ANTIGEN RECOGNITION
Components
  • TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain
  • TCR Variable Delta 1 chain and TCR constant Alpha chain
KeywordsIMMUNE SYSTEM / Immunity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPellicci, D.G. / Uldrich, A.P. / Le Nours, J. / Ross, F. / Chabrol, E. / Eckle, S.B.G. / de Boer, R. / Lim, R.T. / McPherson, K. / Besra, G. ...Pellicci, D.G. / Uldrich, A.P. / Le Nours, J. / Ross, F. / Chabrol, E. / Eckle, S.B.G. / de Boer, R. / Lim, R.T. / McPherson, K. / Besra, G. / Howell, A.R. / Moretta, L. / McCluskey, J. / Heemskerk, M.H.M. / Gras, S. / Rossjohn, J. / Godfrey, D.I.
CitationJournal: J.Exp.Med. / Year: 2014
Title: The molecular bases of delta / alpha beta T cell-mediated antigen recognition.
Authors: Pellicci, D.G. / Uldrich, A.P. / Le Nours, J. / Ross, F. / Chabrol, E. / Eckle, S.B. / de Boer, R. / Lim, R.T. / McPherson, K. / Besra, G. / Howell, A.R. / Moretta, L. / McCluskey, J. / ...Authors: Pellicci, D.G. / Uldrich, A.P. / Le Nours, J. / Ross, F. / Chabrol, E. / Eckle, S.B. / de Boer, R. / Lim, R.T. / McPherson, K. / Besra, G. / Howell, A.R. / Moretta, L. / McCluskey, J. / Heemskerk, M.H. / Gras, S. / Rossjohn, J. / Godfrey, D.I.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / 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 / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 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: TCR Variable Delta 1 chain and TCR constant Alpha chain
B: TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain
C: TCR Variable Delta 1 chain and TCR constant Alpha chain
D: TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain


Theoretical massNumber of molelcules
Total (without water)101,0514
Polymers101,0514
Non-polymers00
Water9,818545
1
A: TCR Variable Delta 1 chain and TCR constant Alpha chain
B: TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain


Theoretical massNumber of molelcules
Total (without water)50,5262
Polymers50,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-23 kcal/mol
Surface area20960 Å2
MethodPISA
2
C: TCR Variable Delta 1 chain and TCR constant Alpha chain
D: TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain


Theoretical massNumber of molelcules
Total (without water)50,5262
Polymers50,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-23 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.257, 47.235, 109.290
Angle α, β, γ (deg.)88.32, 79.78, 89.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TCR Variable Delta 1 chain and TCR constant Alpha chain


Mass: 23186.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein TCR Variable Beta 2 (TRBV20) chain and TCR constant Beta chain


Mass: 27339.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 27% PEG 1500, 0.1M Sodium Malonate-Imidazole-Borate (2:3:3 molar ratio)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.8→53.75 Å / Num. obs: 69885 / % possible obs: 96.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.81 Å2 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / % possible all: 96.4

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.21 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3537 5.06 %RANDOM
Rwork0.193 ---
obs0.195 69881 97.6 %-
Displacement parametersBiso mean: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.6374 Å2-2.1036 Å20.7093 Å2
2--2.3248 Å2-0.6176 Å2
3----3.9621 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 0 545 7496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017219HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089841HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3338SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes181HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1063HARMONIC5
X-RAY DIFFRACTIONt_it7219HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion953SEMIHARMONIC5
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_contact8448SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2456 252 5.01 %
Rwork0.2199 4778 -
all0.2212 5030 -
obs--97.64 %
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)
10.68390.0752-0.04131.0595-0.470.43610.02660.0094-0.0032-0.1051-0.05440.00780.0340.05430.0278-0.05480.00710.0204-0.0023-0.0136-0.0653175.732-223.55381.6069
20.48940.1334-0.1570.5837-0.33030.6994-0.0360.014-0.0186-0.15590.04870.01980.0702-0.0044-0.0127-0.0346-0.00620.0014-0.0162-0.0209-0.0859160.2262-224.27-9.5604
30.4954-0.0702-0.07341.10420.49830.52220.0387-0.0024-0.0350.1214-0.0861-0.00760.0558-0.03410.0474-0.0544-0.04190.02080.00210.0165-0.07156.8493-199.85843.2285
40.5028-0.2013-0.24230.52730.50590.89880.0013-0.00750.00280.12390.0057-0.03390.0752-0.0115-0.007-0.0178-0.0530.0047-0.01330.0169-0.0863172.3439-200.624254.4052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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