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- PDB-8x6b: Crystal structure of immune receptor PVRIG in complex with ligand... -

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Basic information

Entry
Database: PDB / ID: 8x6b
TitleCrystal structure of immune receptor PVRIG in complex with ligand Nectin-2
Components
  • Nectin-2
  • Transmembrane protein PVRIG
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell ...sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / cilium organization / zonula adherens / adhesion of symbiont to host / positive regulation of natural killer cell mediated cytotoxicity / cell-cell contact zone / Adherens junctions interactions / fertilization / apical junction complex / negative regulation of T cell receptor signaling pathway / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / spermatid development / 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 / virus receptor activity / signaling receptor 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. / Immunoglobulin-like domain ...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 Å
AuthorsHu, S.T. / Han, P. / Wang, H. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2024
Title: Structural basis for the immune recognition and selectivity of the immune receptor PVRIG for ligand Nectin-2.
Authors: Hu, S. / Han, P. / Wang, M. / Cao, X. / Liu, H. / Zhang, S. / Zhang, S. / Liu, J. / Han, Y. / Xiao, J. / Chen, Q. / Miao, K. / Qi, J. / Tan, S. / Gao, G.F. / Wang, H.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7713
Polymers28,5502
Non-polymers2211
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-9 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.974, 80.974, 82.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

21A-258-

HOH

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Components

#1: Protein Transmembrane protein PVRIG / CD112 receptor / CD112R / Poliovirus receptor-related immunoglobulin domain-containing protein


Mass: 14599.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRIG, C7orf15 / Production host: Baculovirus transfer vector pFASTBAC1 / References: UniProt: Q6DKI7
#2: Protein Nectin-2


Mass: 13950.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92692
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6 M magnesium sulfate heptahydrate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2→57.87 Å / Num. obs: 26249 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 28.37 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3764

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.49 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 990 5.16 %
Rwork0.204 18188 -
obs0.2058 19178 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.08 Å2
Refinement stepCycle: LAST / Resolution: 2→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 14 122 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631798
X-RAY DIFFRACTIONf_angle_d0.97712452
X-RAY DIFFRACTIONf_chiral_restr0.0602272
X-RAY DIFFRACTIONf_plane_restr0.008319
X-RAY DIFFRACTIONf_dihedral_angle_d6.9762245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.24811480.20612543X-RAY DIFFRACTION100
2.11-2.240.23241200.20852558X-RAY DIFFRACTION100
2.24-2.410.2421140.21722580X-RAY DIFFRACTION100
2.41-2.650.27331260.22912573X-RAY DIFFRACTION99.96
2.65-3.040.25931280.22212610X-RAY DIFFRACTION100
3.04-3.820.21261750.19072591X-RAY DIFFRACTION100
3.83-40.490.23971790.1942733X-RAY DIFFRACTION99.76
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)
12.000260198946.137241304564.254193467197.66030766194-1.754954975274.14887015079-0.469996826151.17484702261-1.69954516216-0.3613761333710.39558414435-0.3634662568830.490072459090.4120565346770.07311159178690.3104173487910.0149063187343-0.006455464302660.221437772753-0.1158353266810.2721578047769.0545114714226.20894091830.8230529703
26.7107670746-1.679943809085.942651033866.16154908314-1.047684609848.096019794220.0554919999657-0.39389391767-0.894974726977-0.02584777062430.3437972988941.16701822429-0.0126674821169-0.825919092072-0.4020223298390.2622249056340.009829925115020.06373381439530.2410070826490.02834213376090.3930855792951.84158305526.623217417635.3201535891
33.391460347680.276634764077-2.390985978384.636393800870.3543927721545.04002604887-0.174825057235-0.188159955482-0.3208047075360.4500006537840.1844558731140.3942648795480.305294885103-0.122227860551-0.02519584462190.1968356093690.02052844484870.009137277310390.1580089470420.0296239315980.1864438978096.4829576424632.442630852542.5620614962
47.602543388892.64348902315-2.382101719645.68438907066-6.389321745349.620032112720.0787064699894-0.002279724800160.641430588730.467648490690.8437888653411.49797498009-0.127566982565-1.71769514131-0.9197195876340.36787554772-0.008157111119690.001591188841490.4973578981090.197949580990.55291191332-5.4752582429635.540261649330.4725478469
55.83441702797-2.270233830725.247587133782.70690979713-2.749139108876.395450789750.3661303719720.512321642161-0.343332710795-0.219778347918-0.01232888949040.1412727362070.5523183795210.131238215443-0.3625396733920.1812787276330.0263538547566-0.007433337804990.169177302958-0.02306137816710.16777690609912.012739593732.273962632733.5936176024
65.888528826861.68609545585-2.496380002854.03970886157-1.753523468663.712046815050.5418685843740.5112285460451.33168825238-0.5547568526420.09318741583950.0545587841046-0.859697257882-0.355714411152-0.6328759640890.6923654879620.0320861631029-0.009582537846340.2199236394140.04809518292780.49674762926426.365406218954.202562605436.6639964377
77.087419116491.05212704512-2.577809157464.29933511403-1.669229677133.686690797420.01547424498030.0682064226760.405416413776-0.312647759082-0.03172466347410.122236466727-0.2465244086930.01695135438710.03094296060590.2725621440430.00302666466346-0.06710471188930.1436437431680.03664173477780.22044568610622.400315421843.712459467439.9737714649
87.04800915834-0.1797601106-1.028919121886.575596471550.08947763346346.523635011430.0241889102502-0.6013225665140.2227280038770.670611111439-0.126623358359-0.18505160145-0.1375927326290.4936071274090.1054476704460.22665973644-0.00957747997332-0.0472351547590.1604494050720.0148466002490.20254472219629.778219889738.83953524144.9830784684
92.011529623172.08614730969-5.798919362733.45199058334-1.915221482585.972508847990.04292102343290.7812511760320.722031773661-0.4492355034330.22537516628-0.0022063917766-0.402534857389-0.353150375824-0.224467576690.3941197118310.00113032573922-0.03758324505460.3139475281480.08804255943230.29272393739424.474124856146.575961495234.975895762
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 3 through 11 )BA3 - 111 - 9
22chain 'B' and (resid 12 through 27 )BA12 - 2710 - 20
33chain 'B' and (resid 28 through 80 )BA28 - 8021 - 73
44chain 'B' and (resid 81 through 93 )BA81 - 9374 - 82
55chain 'B' and (resid 94 through 114 )BA94 - 11483 - 103
66chain 'A' and (resid 3 through 19 )AC3 - 191 - 17
77chain 'A' and (resid 20 through 50 )AC20 - 5018 - 48
88chain 'A' and (resid 51 through 94 )AC51 - 9449 - 92
99chain 'A' and (resid 95 through 128 )AC95 - 12893 - 126

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