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Basic information

Entry
Database: PDB / ID: 2eyt
TitleA structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition
Components(NKT15) x 2
KeywordsIMMUNE SYSTEM / Natural killer T cell receptor / NKT cell receptor / NKT15
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 / Immunoglobulins / Immunoglobulin-like fold ...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: 2.6 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: 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: NKT15
B: NKT15
C: NKT15
D: NKT15


Theoretical massNumber of molelcules
Total (without water)102,1354
Polymers102,1354
Non-polymers00
Water57632
1
A: NKT15
B: NKT15


Theoretical massNumber of molelcules
Total (without water)51,0682
Polymers51,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-23 kcal/mol
Surface area21070 Å2
MethodPISA
2
C: NKT15
D: NKT15


Theoretical massNumber of molelcules
Total (without water)51,0682
Polymers51,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-22 kcal/mol
Surface area21160 Å2
MethodPISA
3
A: NKT15
B: NKT15

C: NKT15
D: NKT15


Theoretical massNumber of molelcules
Total (without water)102,1354
Polymers102,1354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area12810 Å2
ΔGint-49 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.672, 66.672, 182.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody NKT15


Mass: 23365.803 Da / Num. of mol.: 2
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 NKT15


Mass: 27701.801 Da / Num. of mol.: 2
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: Q6GMR4, UniProt: A0A5B9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 6.6
Details: 0.2M sodium sulfate, 20% PEG 3350, pH 6.6, 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: Nov 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→60.86 Å / Num. obs: 27619 / Observed criterion σ(F): 0
Reflection shellResolution: 2.6→2.65 Å / % possible all: 98.53

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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: 2.6→60.86 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 30.363 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25572 1384 5 %RANDOM
Rwork0.20712 ---
all0.21186 ---
obs0.20955 26083 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.008 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.83 Å20 Å2
2--1.66 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7054 0 0 32 7086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9399886
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09124.35354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.011151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1041544
X-RAY DIFFRACTIONr_chiral_restr0.0750.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22861
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24827
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.2190
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.66134586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34257254
X-RAY DIFFRACTIONr_scbond_it3.74773078
X-RAY DIFFRACTIONr_scangle_it5.265102632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 97 -
Rwork0.31 1943 -
obs--97.51 %

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