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- PDB-2eyr: A structural basis for selection and cross-species reactivity of ... -

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Basic information

Entry
Database: PDB / ID: 2eyr
TitleA structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition
Components(NKT12) x 2
KeywordsIMMUNE SYSTEM / Natural killer T cell receptor / NKT cell receptor / NKT12
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / plasma membrane
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 beta constant 2 / T cell receptor alpha chain constant / : / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKjer-Nielsen, L. / Borg, N.A.
CitationJournal: J.Exp.Med. / Year: 2006
Title: A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition
Authors: Kjer-Nielsen, L. / Borg, N.A. / Pellicci, D.G. / Beddoe, T. / Kostenko, L. / Clements, C.S. / Williamson, N.A. / Smyth, M.J. / Besra, G.S. / Reid, H.H. / Bharadwaj, M. / Godfrey, D.I. / ...Authors: Kjer-Nielsen, L. / Borg, N.A. / Pellicci, D.G. / Beddoe, T. / Kostenko, L. / Clements, C.S. / Williamson, N.A. / Smyth, M.J. / Besra, G.S. / Reid, H.H. / Bharadwaj, M. / Godfrey, D.I. / Rossjohn, J. / McCluskey, J.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NKT12
B: NKT12


Theoretical massNumber of molelcules
Total (without water)50,8572
Polymers50,8572
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-21 kcal/mol
Surface area20840 Å2
MethodPISA
2
A: NKT12
B: NKT12

A: NKT12
B: NKT12


Theoretical massNumber of molelcules
Total (without water)101,7154
Polymers101,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11910 Å2
ΔGint-47 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 131.389, 117.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-266-

HOH

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Components

#1: Antibody NKT12


Mass: 23365.803 Da / Num. of mol.: 1 / Mutation: T164C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6PIZ8, UniProt: P01848*PLUS
#2: Protein NKT12


Mass: 27491.525 Da / Num. of mol.: 1 / Mutation: S174C, C192A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q2YDB4, UniProt: A0A5B9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG 3350, 0.1M cacodylate, 0.2M lithium chloride, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→65.65 Å / Num. obs: 18076 / Observed criterion σ(F): 0
Reflection shellResolution: 2.4→2.65 Å / % possible all: 98.74

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MI5

1mi5


Resolution: 2.4→65.65 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.898 / SU B: 21.058 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.693 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27118 1314 7.3 %RANDOM
Rwork0.23034 ---
all0.23336 ---
obs0.232 16747 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--0 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 55 3567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213618
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9384924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19124.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97815588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5341522
X-RAY DIFFRACTIONr_chiral_restr0.0640.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022798
X-RAY DIFFRACTIONr_nbd_refined0.1840.21357
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.27
X-RAY DIFFRACTIONr_mcbond_it0.92732281
X-RAY DIFFRACTIONr_mcangle_it1.69253616
X-RAY DIFFRACTIONr_scbond_it2.34871531
X-RAY DIFFRACTIONr_scangle_it3.418101308
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 86 -
Rwork0.325 1177 -
obs--95.54 %
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)
14.1025-2.6817-0.80445.33940.16691.19440.0587-0.0278-0.0405-0.0753-0.0710.4299-0.0742-0.13870.0122-0.12520.0293-0.02140.01870.0058-0.0905-13.8559.77851.324
211.5177-1.6247-0.83381.5166-0.10761.6014-0.0449-0.50620.45010.18650.1921-0.1005-0.1292-0.05-0.1472-0.06940.05380.0179-0.1129-0.0579-0.0540.71827.21342.819
35.82740.87990.66764.8173-1.87053.8093-0.07930.053-0.26910.38950.0508-0.5368-0.06270.16730.0285-0.10920.06820.0163-0.1551-0.0318-0.0115.533-9.28846.695
41.52551.7969-0.16433.9268-0.78180.8178-0.28980.1013-0.1226-0.28340.1992-0.36270.13840.10750.0906-0.11230.00310.0805-0.0157-0.0497-0.013215.7472.50334.422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1174 - 117
2X-RAY DIFFRACTION2BB3 - 1221 - 116
3X-RAY DIFFRACTION3AA118 - 204118 - 204
4X-RAY DIFFRACTION4BB123 - 247117 - 241

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