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- PDB-3omz: Crystal structure of MICA-specific human gamma delta T cell receptor -

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Basic information

Entry
Database: PDB / ID: 3omz
TitleCrystal structure of MICA-specific human gamma delta T cell receptor
Componentshuman Vdelta1 gamma delta T cell receptor delta1A/B-3
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Immune surveillance of cell stress protein MIC-A/B / MIC-A/B binding / Epithelium
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.04 Å
AuthorsXu, B. / Holmes, M.A. / Strong, R.K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of a {gamma}{delta} T-cell receptor specific for the human MHC class I homolog MICA.
Authors: Xu, B. / Pizarro, J.C. / Holmes, M.A. / McBeth, C. / Groh, V. / Spies, T. / Strong, R.K.
#1: Journal: Science / Year: 1998
Title: Recognition of stress-induced MHC molecules by intestinal epithelial gamma delta T cells
Authors: Groh, V. / Steinle, A. / Bauer, S. / Spies, T.
#2: Journal: Immunity / Year: 1999
Title: Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand
Authors: Li, P. / Willie, S.T. / Bauer, S. / Morris, D.L. / Spies, T. / Strong, R.K.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: human Vdelta1 gamma delta T cell receptor delta1A/B-3
C: human Vdelta1 gamma delta T cell receptor delta1A/B-3
E: human Vdelta1 gamma delta T cell receptor delta1A/B-3
G: human Vdelta1 gamma delta T cell receptor delta1A/B-3


Theoretical massNumber of molelcules
Total (without water)116,9324
Polymers116,9324
Non-polymers00
Water00
1
A: human Vdelta1 gamma delta T cell receptor delta1A/B-3


Theoretical massNumber of molelcules
Total (without water)29,2331
Polymers29,2331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: human Vdelta1 gamma delta T cell receptor delta1A/B-3


Theoretical massNumber of molelcules
Total (without water)29,2331
Polymers29,2331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: human Vdelta1 gamma delta T cell receptor delta1A/B-3


Theoretical massNumber of molelcules
Total (without water)29,2331
Polymers29,2331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: human Vdelta1 gamma delta T cell receptor delta1A/B-3


Theoretical massNumber of molelcules
Total (without water)29,2331
Polymers29,2331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.370, 112.370, 108.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
human Vdelta1 gamma delta T cell receptor delta1A/B-3


Mass: 29232.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL
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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.4M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, 0.03M glycyl-glycyl-glycine, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2007 / Details: Dual crystal, Si(111)
RadiationMonochromator: Dual crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. all: 25563 / Num. obs: 25563 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 48.4
Reflection shellResolution: 3.04→3.16 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.04→32.83 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.849 / SU B: 39.567 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R: 0.849 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30779 1324 5.1 %RANDOM
Rwork0.26514 ---
obs0.26728 24654 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 90.023 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 3.04→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 0 4999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215108
X-RAY DIFFRACTIONr_bond_other_d0.0040.023148
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9296946
X-RAY DIFFRACTIONr_angle_other_deg0.8143.0047576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92822.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.38315620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.141518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
X-RAY DIFFRACTIONr_nbd_refined0.240.31039
X-RAY DIFFRACTIONr_nbd_other0.2360.33159
X-RAY DIFFRACTIONr_nbtor_refined0.2160.52338
X-RAY DIFFRACTIONr_nbtor_other0.10.52922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.5218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.322
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.80323480
X-RAY DIFFRACTIONr_mcbond_other0.13721426
X-RAY DIFFRACTIONr_mcangle_it1.41435261
X-RAY DIFFRACTIONr_scbond_it1.83841981
X-RAY DIFFRACTIONr_scangle_it2.76561685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.037→3.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 111 -
Rwork0.31 1779 -
obs--99.84 %
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)
13.5281-0.09080.51248.7687-3.7114.21180.41840.44150.1418-0.5227-0.10910.34270.2830.0804-0.30930.34650.0430.01390.21950.05940.1707-15.40648.66-8.195
24.66981.22860.3914.8952-1.46163.14960.4898-0.18770.2740.5456-0.09780.9723-0.2704-0.196-0.39190.3285-0.07670.03550.17540.0080.2711-23.40239.2227.613
37.1558-3.2444-2.91193.75773.38074.25810.40981.3686-0.3952-0.1869-0.1391-0.18860.0288-0.4306-0.27080.31510.0373-0.02020.3988-0.13730.053-39.4435.006-8.804
44.15981.2901-0.3651.90860.19242.46760.4717-0.11080.16040.2109-0.2503-0.04110.01140.1322-0.22140.3479-0.08640.10550.1962-0.07050.2517-36.12115.4558.809
55.4783.8597-0.20085.61412.34515.9380.27620.03190.15310.3016-0.0715-0.236-0.76131.0312-0.20470.4395-0.3138-0.0170.46110.13420.1114-43.6055.903-46.711
64.8185-0.3968-0.91043.42131.98355.75940.32360.9587-0.2848-0.64530.3793-1.2371-0.74262.1201-0.70290.2398-0.39670.17531.2893-0.03290.3779-30.6581.097-59.764
73.08020.1133-1.61975.663-3.313112.75580.16170.5371-0.44790.04790.5640.78620.5708-1.2231-0.72570.65370.1668-0.23710.3845-0.04790.0627-18.4352.518-47.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 105
2X-RAY DIFFRACTION2A106 - 250
3X-RAY DIFFRACTION3C11 - 100
4X-RAY DIFFRACTION4C101 - 250
5X-RAY DIFFRACTION5E13 - 108
6X-RAY DIFFRACTION6E109 - 247
7X-RAY DIFFRACTION7G12 - 241

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