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- PDB-3ucr: Crystal structure of the immunoreceptor TIGIT IgV domain -

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Basic information

Entry
Database: PDB / ID: 3ucr
TitleCrystal structure of the immunoreceptor TIGIT IgV domain
ComponentsT cell immunoreceptor with Ig and ITIM domains
KeywordsSIGNALING PROTEIN / PVR/TIGIT/Nectins/Ig superfamily/Signal transduction / IgSF / Immuno receptor / PVR / Nectin-2 / Nectin-3 / Membrane protein
Function / homology
Function and homology information


negative regulation of T cell activation / negative regulation of interleukin-12 production / positive regulation of interleukin-10 production / signaling receptor binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
T-cell immunoglobulin and ITIM domain receptor / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...T-cell immunoglobulin and ITIM domain receptor / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 immunoreceptor with Ig and ITIM domains
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.627 Å
AuthorsYin, J.P. / Stengel, K.F. / Rouge, L. / Bazan, J.F. / Wiesmann, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of TIGIT immunoreceptor bound to poliovirus receptor reveals a cell-cell adhesion and signaling mechanism that requires cis-trans receptor clustering.
Authors: Stengel, K.F. / Harden-Bowles, K. / Yu, X. / Rouge, L. / Yin, J. / Comps-Agrar, L. / Wiesmann, C. / Bazan, J.F. / Eaton, D.L. / Grogan, J.L.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T cell immunoreceptor with Ig and ITIM domains
B: T cell immunoreceptor with Ig and ITIM domains
C: T cell immunoreceptor with Ig and ITIM domains
D: T cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,19312
Polymers47,9094
Non-polymers2848
Water25214
1
A: T cell immunoreceptor with Ig and ITIM domains
C: T cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0966
Polymers23,9552
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-40 kcal/mol
Surface area10740 Å2
MethodPISA
2
B: T cell immunoreceptor with Ig and ITIM domains
D: T cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0966
Polymers23,9552
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-43 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.964, 99.964, 117.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
T cell immunoreceptor with Ig and ITIM domains / V-set and immunoglobulin domain-containing protein 9 / V-set and transmembrane domain-containing protein 3


Mass: 11977.288 Da / Num. of mol.: 4 / Fragment: UNP residues 23-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIGIT, VSIG9, VSTM3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q495A1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M (NH4)2SO4 and 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.627→29.045 Å / Num. all: 20736 / Num. obs: 20690 / % possible obs: 99.93 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2
Reflection shellResolution: 2.627→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2732 / % possible all: 67

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.627→29.045 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1064 5.14 %Random 5%
Rwork0.2155 ---
all0.2184 20736 --
obs0.2184 20690 99.93 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.476 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7763 Å2-0 Å2-0 Å2
2--4.7763 Å20 Å2
3----9.5527 Å2
Refinement stepCycle: LAST / Resolution: 2.627→29.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 8 14 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093331
X-RAY DIFFRACTIONf_angle_d1.1834542
X-RAY DIFFRACTIONf_dihedral_angle_d15.1021156
X-RAY DIFFRACTIONf_chiral_restr0.074530
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6271-2.74660.35291330.3032400X-RAY DIFFRACTION100
2.7466-2.89130.43121230.30032422X-RAY DIFFRACTION100
2.8913-3.07220.33761430.27692422X-RAY DIFFRACTION100
3.0722-3.30910.34871450.25782412X-RAY DIFFRACTION100
3.3091-3.64160.27251300.21682431X-RAY DIFFRACTION100
3.6416-4.16720.23651340.18712468X-RAY DIFFRACTION100
4.1672-5.24520.18511490.14782462X-RAY DIFFRACTION100
5.2452-29.04670.27951070.21062609X-RAY DIFFRACTION100

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