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- PDB-6isa: mCD226 -

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Basic information

Entry
Database: PDB / ID: 6isa
TitlemCD226
ComponentsCD226 antigen
KeywordsIMMUNE SYSTEM / Ig domain / NK cell receptor / DNAM-1
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of immunoglobulin mediated immune response / positive regulation of natural killer cell cytokine production / positive regulation of mast cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of T cell receptor signaling pathway / cell adhesion molecule binding / positive regulation of type II interferon production ...positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of immunoglobulin mediated immune response / positive regulation of natural killer cell cytokine production / positive regulation of mast cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of T cell receptor signaling pathway / cell adhesion molecule binding / positive regulation of type II interferon production / integrin binding / cell adhesion / external side of plasma membrane / protein kinase binding / cell surface / identical protein binding
Similarity search - Function
CD226 antigen / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 China31390432 China
National Natural Science Foundation of China31700149 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: CD226 antigen


Theoretical massNumber of molelcules
Total (without water)25,3711
Polymers25,3711
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.319, 65.771, 70.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na HEPES (pH 7.5), 10 % (w/v) PEG 8000, and 8% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16031 / % possible obs: 97.6 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rsym value: 0.088 / Net I/σ(I): 17.117
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.27 / Num. unique obs: 1536 / CC1/2: 0.953 / Rpim(I) all: 0.128 / Rsym value: 0.27 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ISB
Resolution: 2→40.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33
RfactorNum. reflection% reflection
Rfree0.2399 737 4.71 %
Rwork0.2135 --
obs0.2148 15660 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 140 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021844
X-RAY DIFFRACTIONf_angle_d0.5272519
X-RAY DIFFRACTIONf_dihedral_angle_d22.276681
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.003318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9979-2.15220.28461220.23352675X-RAY DIFFRACTION87
2.1522-2.36880.29811360.24183001X-RAY DIFFRACTION97
2.3688-2.71150.29391400.25313050X-RAY DIFFRACTION98
2.7115-3.41590.24711720.22413066X-RAY DIFFRACTION99
3.4159-40.95840.19611670.17993131X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 6.9386 Å / Origin y: -2.8791 Å / Origin z: 19.9684 Å
111213212223313233
T0.1138 Å20.0006 Å20.0016 Å2-0.1026 Å2-0.0154 Å2--0.0911 Å2
L0.8112 °20.0851 °20.1689 °2-0.4163 °2-0.1105 °2--0.2423 °2
S0.0279 Å °0.0006 Å °-0.0282 Å °-0.022 Å °0.0042 Å °-0.0244 Å °0.0161 Å °-0.01 Å °0.0016 Å °
Refinement TLS groupSelection details: all

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