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- PDB-6isc: complex structure of mCD226-ecto and hCD155-D1 -

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Basic information

Entry
Database: PDB / ID: 6isc
Titlecomplex structure of mCD226-ecto and hCD155-D1
Components
  • CD226 antigen
  • Poliovirus receptor
KeywordsIMMUNE SYSTEM / complex structure / mCD226 / CD155 / NK cell receptor
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell cytokine production / positive regulation of mast cell activation / regulation of viral entry into host cell ...positive regulation of Fc receptor mediated stimulatory signaling pathway / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell cytokine production / 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 / positive regulation of natural killer cell mediated cytotoxicity / apical junction complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / cytoskeleton organization / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / integrin binding / virus receptor activity / signaling receptor activity / cell adhesion / fusion of virus membrane with host plasma membrane / external side of plasma membrane / focal adhesion / protein kinase binding / cell surface / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD226 antigen / 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 ...CD226 antigen / 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
Poliovirus receptor / CD226 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, H. / Qi, J. / Zhang, S. / Li, Y. / Tan, S. / Gao, G.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700149 China
National Natural Science Foundation of China31390432 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Binding mode of the side-by-side two-IgV molecule CD226/DNAM-1 to its ligand CD155/Necl-5.
Authors: Wang, H. / Qi, J. / Zhang, S. / Li, Y. / Tan, S. / Gao, G.F.
History
DepositionNov 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: CD226 antigen
B: Poliovirus receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6883
Polymers38,4672
Non-polymers2211
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-4 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 78.303, 184.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-740-

HOH

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Components

#1: Protein CD226 antigen / Platelet and T-cell activation antigen 1


Mass: 25370.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd226, Pta1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K4F0
#2: Protein Poliovirus receptor / Nectin-like protein 5 / NECL-5


Mass: 13095.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P15151
#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: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (pH 8.0), 0.15 M ammonium sulfate, and 15% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18895 / % possible obs: 99.5 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.036 / Rsym value: 0.099 / Net I/σ(I): 23.456
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Num. unique obs: 1772 / CC1/2: 0.798 / Rpim(I) all: 0.378 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ISA, 3EOW

6isa

3eow
PDB Unreleased entry


Resolution: 2.2→42.273 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.2651 972 5.16 %
Rwork0.2331 --
obs0.2347 18851 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 0 164 2847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022760
X-RAY DIFFRACTIONf_angle_d0.4893761
X-RAY DIFFRACTIONf_dihedral_angle_d20.251009
X-RAY DIFFRACTIONf_chiral_restr0.042426
X-RAY DIFFRACTIONf_plane_restr0.004477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1981-2.31390.36521590.30472390X-RAY DIFFRACTION95
2.3139-2.45890.3171260.28662527X-RAY DIFFRACTION100
2.4589-2.64870.30981480.28692527X-RAY DIFFRACTION100
2.6487-2.91520.28541520.26342556X-RAY DIFFRACTION100
2.9152-3.33690.31591180.24442590X-RAY DIFFRACTION100
3.3369-4.20350.22781540.20772571X-RAY DIFFRACTION100
4.2035-42.28060.2261150.20772718X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.359 Å / Origin y: -14.6221 Å / Origin z: 23.3973 Å
111213212223313233
T0.2291 Å2-0.0234 Å2-0.0322 Å2-0.2487 Å20.0397 Å2--0.2201 Å2
L1.2517 °2-0.2255 °2-0.5085 °2-1.0997 °20.6801 °2--1.519 °2
S-0.05 Å °0.0282 Å °-0.1266 Å °-0.0949 Å °0.0439 Å °-0.0037 Å °-0.009 Å °0.0927 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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