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- PDB-9e6y: Structure of CD112 (Nectin-2) domain 1 bound to CD112R (PVRIG) -

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Basic information

Entry
Database: PDB / ID: 9e6y
TitleStructure of CD112 (Nectin-2) domain 1 bound to CD112R (PVRIG)
Components
  • Nectin-2
  • Transmembrane protein PVRIG
KeywordsIMMUNOSUPPRESSANT / Checkpoint receptor Immunoglobulin folding
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 / positive regulation of mast cell activation / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / regulation of viral entry into host cell / Nectin/Necl trans heterodimerization ...coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / sperm mitochondrion organization / positive regulation of immunoglobulin mediated immune response / positive regulation of mast cell activation / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / regulation of viral entry into host cell / Nectin/Necl trans heterodimerization / acrosome assembly / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / adhesion of symbiont to host / zonula adherens / cilium organization / positive regulation of natural killer cell mediated cytotoxicity / cell-cell contact zone / Adherens junctions interactions / fertilization / negative regulation of natural killer cell mediated cytotoxicity / apical junction complex / negative regulation of T cell receptor signaling pathway / natural killer cell mediated cytotoxicity / positive regulation of T cell receptor signaling pathway / spermatid development / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatase binding / coreceptor activity / cell adhesion molecule binding / cytoskeleton organization / establishment of localization in cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / signaling receptor activity / virus receptor activity / receptor ligand activity / fusion of virus membrane with host plasma membrane / focal adhesion / cell surface / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Transmembrane protein PVRIG / : / 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. ...Transmembrane protein PVRIG / : / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Transmembrane protein PVRIG / Nectin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLuca, V.C. / Singh, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133482-01 United States
CitationJournal: Mol.Ther. / Year: 2025
Title: Structure-guided engineering of CD112 receptor variants for optimized immunotherapy.
Authors: Singh, S. / Julia, E. / Kalita, P. / Mason, C. / Ming, Q. / Lee-Sam, A. / Gordon, S. / Buitrago, M.E. / Leung, D.W. / Hwu, P. / Luca, V.C.
History
DepositionOct 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Nectin-2
A: Transmembrane protein PVRIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,24614
Polymers28,3422
Non-polymers90412
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint9 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.650, 79.650, 81.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Nectin cell adhesion molecule ...Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Nectin cell adhesion molecule 2 / Poliovirus receptor-related protein 2


Mass: 14399.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN2, HVEB, PRR2, PVRL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92692
#2: Protein Transmembrane protein PVRIG / CD112 receptor / CD112R / Poliovirus receptor-related immunoglobulin domain-containing protein


Mass: 13942.655 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRIG, C7orf15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DKI7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES PH 9.5, 20% W/V PEG 8000

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→36.24 Å / Num. obs: 13826 / % possible obs: 99.94 % / Redundancy: 19.57 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 17.6
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1362 / CC1/2: 0.645 / CC star: 0.886

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.24 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 24.351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2454 692 5.01 %
Rwork0.2078 13130 -
obs0.2096 13826 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 58 105 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211908
X-RAY DIFFRACTIONf_angle_d0.56062582
X-RAY DIFFRACTIONf_chiral_restr0.0441287
X-RAY DIFFRACTIONf_plane_restr0.0042332
X-RAY DIFFRACTIONf_dihedral_angle_d4.3594269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2790.24541350.20782553X-RAY DIFFRACTION99.94
2.37-2.610.30341350.25312575X-RAY DIFFRACTION100
2.61-2.990.25791370.23052595X-RAY DIFFRACTION99.96
2.99-3.760.23271390.19562635X-RAY DIFFRACTION100
3.76-36.240.22071460.18682772X-RAY DIFFRACTION99.93

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