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- PDB-6mra: Diversity in the type II Natural Killer T cell receptor repertoir... -

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Basic information

Entry
Database: PDB / ID: 6mra
TitleDiversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies
Components
  • TCR alpha chain
  • TCR beta-chain
KeywordsIMMUNE SYSTEM / NKT cells / CD1d molecule / microbial lipid antigen
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSundararaj, S. / Le Nours, J. / Praveena, T. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2019
Title: Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors.
Authors: Almeida, C.F. / Sundararaj, S. / Le Nours, J. / Praveena, T. / Cao, B. / Burugupalli, S. / Smith, D.G.M. / Patel, O. / Brigl, M. / Pellicci, D.G. / Williams, S.J. / Uldrich, A.P. / Godfrey, D.I. / Rossjohn, J.
History
DepositionOct 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: TCR alpha chain
B: TCR beta-chain


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers50,0562
Non-polymers00
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-26 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.447, 74.229, 115.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TCR alpha chain


Mass: 22644.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein TCR beta-chain


Mass: 27412.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 10-20% PEG3350 4% tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→45.6 Å / Num. obs: 47656 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 24.37 Å2 / Rpim(I) all: 0.029 / Net I/σ(I): 16.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Num. unique obs: 6830 / Rpim(I) all: 0.308 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2408 5.06 %RANDOM
Rwork0.181 ---
obs0.183 47590 100 %-
Displacement parametersBiso mean: 27.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.2206 Å20 Å20 Å2
2--2.607 Å20 Å2
3----1.3864 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.7→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 0 481 3716
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013390HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064644HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1538SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes599HARMONIC5
X-RAY DIFFRACTIONt_it3390HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion2.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
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_contact4221SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.71 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2643 -5.67 %
Rwork0.2157 898 -
all0.2186 952 -
obs--99.08 %
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)
11.40511.13630.06821.4792-0.04180.2696-0.0695-0.0509-0.2556-0.09450.0228-0.1760.0923-0.0030.0467-0.03840.00150.0284-0.0380.0101-0.037338.740773.41614.3462
20.50270.5193-0.24340.9377-0.36210.48650.0539-0.0579-0.02950.1069-0.0577-0.0259-0.0519-0.04890.0038-0.04890.01990.00920.01220.017-0.069233.425978.439621.579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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