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- PDB-4ww1: Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta ... -

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Basic information

Entry
Database: PDB / ID: 4ww1
TitleCrystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
Components
  • TCR Alpha Chain-TRAV21-TRAJ8
  • TCR Beta Chain-TRBV7-8
KeywordsIMMUNE SYSTEM / Immunity / NKT cells
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / alpha-beta T cell activation / response to bacterium / T cell receptor signaling pathway / adaptive immune response / plasma membrane
Similarity search - Function
: / 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. ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21 / T cell receptor beta constant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsLe Nours, J. / Praveena, T. / Pellicci, D.G. / Lim, R.T. / Besra, G. / Howell, A.R. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
CitationJournal: Nat Commun / Year: 2016
Title: Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.
Authors: Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Ross, F.J. / Lim, R.T. / Besra, G.S. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 1.3Oct 23, 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 Alpha Chain-TRAV21-TRAJ8
B: TCR Beta Chain-TRBV7-8


Theoretical massNumber of molelcules
Total (without water)49,9422
Polymers49,9422
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-28 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 73.120, 65.600
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TCR Alpha Chain-TRAV21-TRAJ8


Mass: 22573.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279*PLUS
#2: Protein TCR Beta Chain-TRBV7-8


Mass: 27368.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3000 0.2M Na Acetate 0.1M Tris-HCl 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→37.28 Å / Num. obs: 83037 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 15.28 Å2 / Net I/σ(I): 9.8
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PO6

2po6


Resolution: 1.38→27.6 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.9419 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 4150 5 %RANDOM
Rwork0.193 ---
obs0.194 83037 99.69 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.0554 Å20 Å20.6332 Å2
2--0.4237 Å20 Å2
3---0.6317 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: LAST / Resolution: 1.38→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 461 3971
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013631HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095010HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes566HARMONIC5
X-RAY DIFFRACTIONt_it3631HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.51
X-RAY DIFFRACTIONt_other_torsion2.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
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_contact4460SEMIHARMONIC4
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 295 4.96 %
Rwork0.2103 5656 -
all0.2108 5951 -
obs--99.69 %
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)
10.7141-0.02830.43990.4466-0.18170.7452-0.02320.0218-0.02960.01320.08120.0778-0.0461-0.0867-0.058-0.00880.0120.0125-0.02220.0174-0.0368-0.7918-4.684295.7034
20.0907-0.0606-0.13260.26150.0010.4531-0.0111-0.0094-0.0228-0.0282-0.02470.0006-0.0085-0.03120.0358-0.0128-0.00040.0005-0.0490.0008-0.053414.9455-0.865584.4898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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