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- PDB-6isb: crystal structure of human CD226 -

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Basic information

Entry
Database: PDB / ID: 6isb
Titlecrystal structure of human CD226
ComponentsCD226 antigen
KeywordsIMMUNE SYSTEM / CD226 / DNAM-1
Function / homology
Function and homology information


cell recognition / 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 / positive regulation of T cell receptor signaling pathway / cell adhesion molecule binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...cell recognition / 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 / positive regulation of T cell receptor signaling pathway / cell adhesion molecule binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / integrin binding / cell adhesion / membrane raft / external side of plasma membrane / protein kinase binding / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
CD226 antigen / Immunoglobulin subtype 2 / Immunoglobulin C-2 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWang, H. / Qi, J. / Zhang, S. / Li, Y. / Tan, S. / Gao, G.F.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD226 antigen
B: CD226 antigen
C: CD226 antigen


Theoretical massNumber of molelcules
Total (without water)79,2473
Polymers79,2473
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-13 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.879, 118.492, 123.171
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 / DNAX accessory molecule 1 / DNAM-1


Mass: 26415.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD226, DNAM1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q15762

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M Tris (pH 7.5) and 0.8 M Na/K hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30085 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rsym value: 0.077 / Net I/σ(I): 24.645
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 4.311 / Num. unique obs: 2955 / CC1/2: 0.91 / Rpim(I) all: 0.213 / Rsym value: 0.573 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→42.696 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1
RfactorNum. reflection% reflection
Rfree0.2673 1504 5.01 %
Rwork0.2549 --
obs0.2555 30026 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 0 0 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054478
X-RAY DIFFRACTIONf_angle_d0.8726110
X-RAY DIFFRACTIONf_dihedral_angle_d13.1081611
X-RAY DIFFRACTIONf_chiral_restr0.054678
X-RAY DIFFRACTIONf_plane_restr0.008773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4993-2.580.31361680.30622481X-RAY DIFFRACTION98
2.58-2.67220.28881480.29382529X-RAY DIFFRACTION100
2.6722-2.77920.28931190.28632577X-RAY DIFFRACTION100
2.7792-2.90560.30071220.27472594X-RAY DIFFRACTION100
2.9056-3.05880.30951470.29342540X-RAY DIFFRACTION100
3.0588-3.25030.30281650.27512558X-RAY DIFFRACTION100
3.2503-3.50120.25511030.26352604X-RAY DIFFRACTION100
3.5012-3.85330.27511480.24892595X-RAY DIFFRACTION100
3.8533-4.41040.25971450.22992599X-RAY DIFFRACTION100
4.4104-5.55470.21371000.22092670X-RAY DIFFRACTION100
5.5547-42.70260.25661390.26482775X-RAY DIFFRACTION99

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