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- PDB-5iw1: Crystal Structure of B4.2.3 T-Cell Receptor -

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Basic information

Entry
Database: PDB / ID: 5iw1
TitleCrystal Structure of B4.2.3 T-Cell Receptor
Components
  • T-CELL RECEPTOR ALPHA CHAIN
  • T-CELL RECEPTOR BETA CHAIN
KeywordsIMMUNE SYSTEM / T-cell Receptor / TCR / B4.2.3 / B423 / MHC Class I / MOLECULAR RECOGNITION / HUMAN IMMUNODEFICIENCY VIRUS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsNatarajan, K. / Jiang, J. / Margulies, D.
CitationJournal: Nat Commun / Year: 2017
Title: An allosteric site in the T-cell receptor C beta domain plays a critical signalling role.
Authors: Natarajan, K. / McShan, A.C. / Jiang, J. / Kumirov, V.K. / Wang, R. / Zhao, H. / Schuck, P. / Tilahun, M.E. / Boyd, L.F. / Ying, J. / Bax, A. / Margulies, D.H. / Sgourakis, N.G.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-CELL RECEPTOR ALPHA CHAIN
B: T-CELL RECEPTOR BETA CHAIN
C: T-CELL RECEPTOR ALPHA CHAIN
D: T-CELL RECEPTOR BETA CHAIN
E: T-CELL RECEPTOR ALPHA CHAIN
F: T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)145,7036
Polymers145,7036
Non-polymers00
Water0
1
A: T-CELL RECEPTOR ALPHA CHAIN
B: T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)48,5682
Polymers48,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area20770 Å2
MethodPISA
2
C: T-CELL RECEPTOR ALPHA CHAIN
D: T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)48,5682
Polymers48,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-25 kcal/mol
Surface area20710 Å2
MethodPISA
3
E: T-CELL RECEPTOR ALPHA CHAIN
F: T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)48,5682
Polymers48,5682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-22 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.112, 96.112, 167.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein T-CELL RECEPTOR ALPHA CHAIN


Mass: 21658.111 Da / Num. of mol.: 3 / Mutation: T163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: T LYMPHOCYTE / Cell line: B4.2.3 T CELL HYBRIDOMA / Gene: TCRAV2S6J38 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein T-CELL RECEPTOR BETA CHAIN


Mass: 26909.424 Da / Num. of mol.: 3 / Mutation: S167C, C181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: T LYMPHOCYTE / Cell line: B4.2.3 T CELL HYBRIDOMA / Gene: TCRAV2S6J38 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 16% PEG 4000, 0.1M TRIS, 0.2M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2006
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3→48.1 Å / Num. obs: 32680 / % possible obs: 94.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 70.3 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 65.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IVX

5ivx


Resolution: 3.001→48.056 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 31.01
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1966 6.02 %Random
Rwork0.2402 ---
obs0.243 32680 94.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 91 Å2
Refinement stepCycle: LAST / Resolution: 3.001→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10062 0 0 0 10062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210332
X-RAY DIFFRACTIONf_angle_d0.60813995
X-RAY DIFFRACTIONf_dihedral_angle_d9.983771
X-RAY DIFFRACTIONf_chiral_restr0.0231491
X-RAY DIFFRACTIONf_plane_restr0.0031821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0023-3.07730.3114930.31341464X-RAY DIFFRACTION59
3.0773-3.16050.38191060.31521734X-RAY DIFFRACTION71
3.1605-3.25340.31991210.28982013X-RAY DIFFRACTION81
3.2534-3.35840.28671490.27992254X-RAY DIFFRACTION91
3.3584-3.47830.30231500.27732331X-RAY DIFFRACTION94
3.4783-3.61750.31751620.26482293X-RAY DIFFRACTION93
3.6175-3.7820.27771640.25692309X-RAY DIFFRACTION93
3.782-3.98120.2631410.25182337X-RAY DIFFRACTION94
3.9812-4.23030.24371360.23512347X-RAY DIFFRACTION95
4.2303-4.55640.22721630.18962306X-RAY DIFFRACTION93
4.5564-5.01390.2111290.18772335X-RAY DIFFRACTION95
5.0139-5.73720.25521470.20812328X-RAY DIFFRACTION94
5.7372-7.21980.27051340.23632323X-RAY DIFFRACTION95
7.2198-37.42460.32891390.26032336X-RAY DIFFRACTION94

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