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- PDB-5v52: Structure of TIGIT bound to nectin-2 (CD112) -

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Basic information

Entry
Database: PDB / ID: 5v52
TitleStructure of TIGIT bound to nectin-2 (CD112)
Components
  • Nectin-2
  • T-cell immunoreceptor with Ig and ITIM domains
KeywordsIMMUNE SYSTEM / immune receptor / adhesion molecule / immunoglobulin fold
Function / homology
Function and homology information


coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / positive regulation of mast cell activation / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / Nectin/Necl trans heterodimerization / regulation of viral entry into host cell ...coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / positive regulation of mast cell activation / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / Nectin/Necl trans heterodimerization / regulation of viral entry into host cell / acrosome assembly / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / cilium organization / zonula adherens / adhesion of symbiont to host / negative regulation of T cell activation / positive regulation of natural killer cell mediated cytotoxicity / cell-cell contact zone / negative regulation of interleukin-12 production / Adherens junctions interactions / fertilization / apical junction complex / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of interleukin-10 production / spermatid development / coreceptor activity / cytoskeleton organization / cell adhesion molecule binding / establishment of localization in cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / virus receptor activity / fusion of virus membrane with host plasma membrane / signaling receptor binding / focal adhesion / cell surface / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
T-cell immunoglobulin and ITIM domain receptor / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...T-cell immunoglobulin and ITIM domain receptor / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / 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 / Nectin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDeuss, F.A. / Gully, B.S. / Rossjohn, J. / Berry, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1109901 Australia
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Recognition of nectin-2 by the natural killer cell receptor T cell immunoglobulin and ITIM domain (TIGIT).
Authors: Deuss, F.A. / Gully, B.S. / Rossjohn, J. / Berry, R.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 26, 2020Group: Data collection / Category: chem_comp / reflns / Item: _chem_comp.type / _reflns.pdbx_Rpim_I_all
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Nectin-2
D: Nectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3867
Polymers53,9764
Non-polymers4093
Water00
1
A: T-cell immunoreceptor with Ig and ITIM domains
D: Nectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0803
Polymers26,9882
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area11100 Å2
MethodPISA
2
B: T-cell immunoreceptor with Ig and ITIM domains
C: Nectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3064
Polymers26,9882
Non-polymers3172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-21 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.500, 68.500, 253.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 11671.995 Da / Num. of mol.: 2
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: Protein Nectin-2 / Herpes virus entry mediator B / HveB / Nectin cell adhesion molecule 2 / Poliovirus receptor-related protein 2


Mass: 15316.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN2, HVEB, PRR2, PVRL2 / Production host: Homo sapiens (human) / References: UniProt: Q92692
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M Lithium Sulfate 0.1M Tris ph7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→85 Å / Num. obs: 11784 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 65.19 Å2 / Rpim(I) all: 0.096 / Net I/σ(I): 6.3
Reflection shellResolution: 3.27→3.31 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1677 / Rpim(I) all: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UCR, 3R0N

3ucr

3r0n


Resolution: 3.1→24.65 Å / Cor.coef. Fo:Fc: 0.8944 / Cor.coef. Fo:Fc free: 0.8449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.236 563 4.82 %RANDOM
Rwork0.2176 ---
obs0.2185 11685 99.76 %-
Displacement parametersBiso mean: 71.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.4839 Å20 Å20 Å2
2---6.4839 Å20 Å2
3---12.9677 Å2
Refine analyzeLuzzati coordinate error obs: 0.666 Å
Refinement stepCycle: 1 / Resolution: 3.1→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 25 0 3443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073535HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934858HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1518SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes522HARMONIC5
X-RAY DIFFRACTIONt_it3535HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion2.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3640SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.4 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2588 137 5.05 %
Rwork0.2444 2578 -
all0.2451 2715 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: -8.8222 Å / Origin y: 8.078 Å / Origin z: -28.4634 Å
111213212223313233
T0.0982 Å2-0.0308 Å20.1492 Å2--0.1164 Å20.0387 Å2---0.1881 Å2
L2.2736 °2-0.7912 °2-2.0189 °2-0.3219 °20.752 °2--2.6036 °2
S-0.0361 Å °-0.1277 Å °-0.0245 Å °0.1448 Å °-0.0931 Å °0.056 Å °0.0328 Å °0.2051 Å °0.1293 Å °
Refinement TLS groupSelection details: { *|* }

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