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- PDB-1hxm: Crystal Structure of a Human Vgamma9/Vdelta2 T Cell Receptor -

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Basic information

Entry
Database: PDB / ID: 1hxm
TitleCrystal Structure of a Human Vgamma9/Vdelta2 T Cell Receptor
Components(GAMMA-DELTA T-CELL RECEPTOR) x 2
KeywordsIMMUNE SYSTEM / Ig domain / T cell receptor / TCR / gdTCR
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / T cell receptor complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / plasma membrane => GO:0005886 / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway ...positive regulation of B cell activation / phagocytosis, recognition / T cell receptor complex / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / plasma membrane => GO:0005886 / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / transmembrane signaling receptor activity / adaptive immune response / membrane => GO:0016020 / defense response to bacterium / immune response / external side of plasma membrane / innate immune response
Similarity search - Function
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 delta constant / T cell receptor gamma constant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 3.12 Å
AuthorsAllison, T.J. / Winter, C.C. / Fournie, J.J. / Bonneville, M. / Garboczi, D.N.
Citation
Journal: Nature / Year: 2001
Title: Structure of a human gammadelta T-cell antigen receptor.
Authors: Allison, T.J. / Winter, C.C. / Fournie, J.J. / Bonneville, M. / Garboczi, D.N.
#1: Journal: EUR.J.IMMUNOL. / Year: 1993
Title: Peripheral selection of antigen receptor junctional features in a major human gamma delta subset
Authors: Davodeau, F. / Peyrat, M.A. / Hallet, M.M. / Houde, I. / Vie, H. / Bonneville, M.
#2: Journal: Science / Year: 1994
Title: Stimulation of human gamma delta T cells by nonpeptidic mycobaterial ligands
Authors: Constant, P. / Davodeau, F. / Peyrat, M.A. / Poquet, Y. / Puzo, G. / Bonneville, M. / Fournie, J.J.
History
DepositionJan 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA-DELTA T-CELL RECEPTOR
B: GAMMA-DELTA T-CELL RECEPTOR
C: GAMMA-DELTA T-CELL RECEPTOR
D: GAMMA-DELTA T-CELL RECEPTOR
E: GAMMA-DELTA T-CELL RECEPTOR
F: GAMMA-DELTA T-CELL RECEPTOR
G: GAMMA-DELTA T-CELL RECEPTOR
H: GAMMA-DELTA T-CELL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,77710
Polymers211,5858
Non-polymers1922
Water97354
1
A: GAMMA-DELTA T-CELL RECEPTOR
B: GAMMA-DELTA T-CELL RECEPTOR


Theoretical massNumber of molelcules
Total (without water)52,8962
Polymers52,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-33 kcal/mol
Surface area21300 Å2
MethodPISA
2
C: GAMMA-DELTA T-CELL RECEPTOR
D: GAMMA-DELTA T-CELL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9923
Polymers52,8962
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-34 kcal/mol
Surface area21070 Å2
MethodPISA
3
E: GAMMA-DELTA T-CELL RECEPTOR
F: GAMMA-DELTA T-CELL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9923
Polymers52,8962
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area21190 Å2
MethodPISA
4
G: GAMMA-DELTA T-CELL RECEPTOR
H: GAMMA-DELTA T-CELL RECEPTOR


Theoretical massNumber of molelcules
Total (without water)52,8962
Polymers52,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-22 kcal/mol
Surface area21030 Å2
MethodPISA
5
E: GAMMA-DELTA T-CELL RECEPTOR
F: GAMMA-DELTA T-CELL RECEPTOR
hetero molecules

A: GAMMA-DELTA T-CELL RECEPTOR
B: GAMMA-DELTA T-CELL RECEPTOR


Theoretical massNumber of molelcules
Total (without water)105,8885
Polymers105,7924
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area9700 Å2
ΔGint-70 kcal/mol
Surface area40100 Å2
MethodPISA
6
C: GAMMA-DELTA T-CELL RECEPTOR
D: GAMMA-DELTA T-CELL RECEPTOR
hetero molecules

G: GAMMA-DELTA T-CELL RECEPTOR
H: GAMMA-DELTA T-CELL RECEPTOR


Theoretical massNumber of molelcules
Total (without water)105,8885
Polymers105,7924
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area9540 Å2
ΔGint-70 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.048, 151.736, 97.873
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
GAMMA-DELTA T-CELL RECEPTOR / T-CELL RECEPTOR DELTA CHAIN


Mass: 25535.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VD2, DD3, JD1, CD / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PUBS / References: GenBank: 298105, UniProt: B7Z8K6*PLUS
#2: Protein
GAMMA-DELTA T-CELL RECEPTOR / T-CELL RECEPTOR GAMMA CHAIN


Mass: 27360.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VG9, JGP, CG1 / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PUBS / References: UniProt: P03986
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG4000, 0.2 M Li2SO4, 0.1 M Tris-HCl, 20% glycerol, 4 mg/mL protein, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
228 %PEG40001drop
30.2 M1dropLi2SO4
40.1 MTris-HCl1drop
520 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2000 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. all: 42118 / Num. obs: 42118 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 20.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 60 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 3.12→30.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1900398.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Initial model was built into and refined against a 3.25 Angstroms SeMet MAD data set (same space group with very similar unit cell). That model was then brought into this unit cell and ...Details: Initial model was built into and refined against a 3.25 Angstroms SeMet MAD data set (same space group with very similar unit cell). That model was then brought into this unit cell and refined against this 3.12 Angstroms data.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1938 5.2 %SHELLS
Rwork0.219 ---
obs0.219 37543 99 %-
all-40945 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0227 Å2 / ksol: 0.298879 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-24.14 Å20 Å27.44 Å2
2---19.46 Å20 Å2
3----4.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.12→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13756 0 10 54 13820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it4.451.5
X-RAY DIFFRACTIONc_mcangle_it7.32
X-RAY DIFFRACTIONc_scbond_it5.982
X-RAY DIFFRACTIONc_scangle_it8.72.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINED GROUP 1 MAINCHAIN ATOMS OF V DELTA DOMAINS, RESIDUES 1-24, 36-50, 56-68, 75-93, AND 109-118 FROM CHAINS A, C, E, AND G GROUP 2 MAINCHAIN ATOMS OF V GAMMA DOMAINS, RESIDUES 1-24, 35-52, 58-72, 80-99, AND 112-122 FROM CHAINS B, D, F, AND H GROUP 3 MAINCHAIN ATOMS OF C DELTA DOMAINS, RESIDUES 125-206 FROM CHAINS A, C, E, AND G GROUP 4 MAINCHAIN ATOMS OF C GAMMA DOMAINS, RESIDUES 130-168 AND 176-230 FROM CHAINS B, D, F, AND H GROUP 5 SIDECHAIN ATOMS OF V DELTA DOMAINS, RESIDUES 1-24, 36-50, 56-60, 62-68, 75-77, 79-93, AND 109-118 FROM CHAINS A, C, E, AND G GROUP 6 SIDECHAIN ATOMS OF V GAMMA DOMAINS, RESIDUES 1-16, 18-24, 35-52, 58-72, 80-88, 90-99, AND 112-122 FROM CHAINS B, D, F, AND H GROUP 7 SIDECHAIN ATOMS OF C DELTA DOMAINS, RESIDUES 125-157 AND 159-206 FROM CHAINS A, C, E, AND G GROUP 8 SIDECHAIN ATOMS OF C GAMMA DOMAINS, RESIDUES 130-146, 149-168, 176-208, AND 210-230 FROM CHAINS B, D, F, AND H8.830.03200
226.020.04200
335.850.03200
444.930.03200
558.60.05100
666.980.08100
776.90.06100
886.070.06100
LS refinement shellResolution: 3.12→3.32 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 300 4.8 %
Rwork0.29 5890 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.29

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