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- PDB-4ei6: Structure of XV19 Valpha1-Vbeta16 Type-II Natural Killer T cell r... -

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Entry
Database: PDB / ID: 4ei6
TitleStructure of XV19 Valpha1-Vbeta16 Type-II Natural Killer T cell receptor
Components
  • Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
  • Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
KeywordsIMMUNE SYSTEM / Natural Killer T cell receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2012
Title: Recognition of CD1d-sulfatide mediated by a type II natural killer T cell antigen receptor.
Authors: Patel, O. / Pellicci, D.G. / Gras, S. / Sandoval-Romero, M.L. / Uldrich, A.P. / Mallevaey, T. / Clarke, A.J. / Le Nours, J. / Theodossis, A. / Cardell, S.L. / Gapin, L. / Godfrey, D.I. / Rossjohn, J.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Sep 13, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
B: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
C: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
D: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Theoretical massNumber of molelcules
Total (without water)102,5804
Polymers102,5804
Non-polymers00
Water14,700816
1
A: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
B: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Theoretical massNumber of molelcules
Total (without water)51,2902
Polymers51,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-28 kcal/mol
Surface area20710 Å2
MethodPISA
2
C: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
D: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Theoretical massNumber of molelcules
Total (without water)51,2902
Polymers51,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-26 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.268, 100.120, 152.668
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 Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Mass: 23209.518 Da / Num. of mol.: 2 / Fragment: extracellular domain (SEE REMARK 999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
#2: Protein Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)


Mass: 28080.617 Da / Num. of mol.: 2 / Fragment: extracellular domain (SEE REMARK 999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAINS A AND C ARE CHIMERAS COMPRISING THE MOUSE VARIABLE DOMAIN (RESIDUES 1-116) AND HUMAN ...CHAINS A AND C ARE CHIMERAS COMPRISING THE MOUSE VARIABLE DOMAIN (RESIDUES 1-116) AND HUMAN CONSTANT DOMAIN (RESIDUES 117-207). CHAINS B AND D ARE CHIMERAS COMPRISING THE MOUSE VARIABLE DOMAIN (RESIDUES 1-114) AND HUMAN CONSTANT DOMAIN (RESIDUES 115-244).

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium malonate/imidazole/boric acid buffer, 25% PEG3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 132448 / Num. obs: 132448 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 21.64 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.001 / Mean I/σ(I) obs: 1.9 / Num. unique all: 19137 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BNU

2bnu


Resolution: 1.6→44.45 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 6662 5.03 %RANDOM
Rwork0.2078 ---
obs0.2095 132448 99.98 %-
all-132448 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.348 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1784 Å2-0 Å20 Å2
2---1.5622 Å2-0 Å2
3---4.7406 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6763 0 0 816 7579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067106
X-RAY DIFFRACTIONf_angle_d1.0599706
X-RAY DIFFRACTIONf_dihedral_angle_d12.9622487
X-RAY DIFFRACTIONf_chiral_restr0.0771050
X-RAY DIFFRACTIONf_plane_restr0.0041267
LS refinement shellResolution: 1.6→1.69 Å
RfactorNum. reflection% reflection
Rfree0.3424 651 -
Rwork0.3228 12447 -
obs-12447 100 %

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