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Yorodumi- PDB-7e72: Crystal structure of Tie2-agonistic antibody in complex with huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+72 | |||||||||
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Title | Crystal structure of Tie2-agonistic antibody in complex with human Tie2 Fn2-3 | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / antigen-antibody complex / agonistic antibody / angiogenesis / vascular stabilization / receptor tyrosine kinase / Tie2 | |||||||||
Function / homology | Function and homology information Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation ...Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of intracellular signal transduction / positive regulation of Rho protein signal transduction / positive regulation of Rac protein signal transduction / growth factor binding / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / transmembrane receptor protein tyrosine kinase activity / negative regulation of endothelial cell apoptotic process / negative regulation of angiogenesis / basal plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / Tie2 Signaling / response to cAMP / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / receptor protein-tyrosine kinase / negative regulation of inflammatory response / response to peptide hormone / response to estrogen / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / signaling receptor activity / heart development / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / receptor complex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / protein kinase activity / positive regulation of protein phosphorylation / apical plasma membrane / membrane raft / focal adhesion / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å | |||||||||
Authors | Kim, H.M. / Jo, G.H. / Hong, H.J. / Han, A. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural insights into the clustering and activation of Tie2 receptor mediated by Tie2 agonistic antibody. Authors: Jo, G. / Bae, J. / Hong, H.J. / Han, A.R. / Kim, D.K. / Hong, S.P. / Kim, J.A. / Lee, S. / Koh, G.Y. / Kim, H.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e72.cif.gz | 518.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e72.ent.gz | 428.6 KB | Display | PDB format |
PDBx/mmJSON format | 7e72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e72_validation.pdf.gz | 501.6 KB | Display | wwPDB validaton report |
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Full document | 7e72_full_validation.pdf.gz | 531.9 KB | Display | |
Data in XML | 7e72_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 7e72_validation.cif.gz | 80.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e72 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e72 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24388.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Antibody | Mass: 23415.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) #3: Protein | Mass: 22355.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q02763, receptor protein-tyrosine kinase #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Bis-Tris propane pH 8.5, 110 mM potassium dihydrogen phosphate, 15% (w/v) polyethylene glycol 3350 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.094→44.72 Å / Num. obs: 84953 / % possible obs: 91.04 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.96 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.126 |
Reflection shell | Resolution: 2.094→2.169 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.217 / Num. unique obs: 8247 / % possible all: 88.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X8M, 5MYA Resolution: 2.094→44.72 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.41 Å2 / Biso mean: 39.2863 Å2 / Biso min: 11.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.094→44.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 34.9749 Å / Origin y: 15.1799 Å / Origin z: 89.5922 Å
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Refinement TLS group |
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