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- PDB-7e72: Crystal structure of Tie2-agonistic antibody in complex with huma... -

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Basic information

Entry
Database: PDB / ID: 7.0E+72
TitleCrystal structure of Tie2-agonistic antibody in complex with human Tie2 Fn2-3
Components
  • Angiopoietin-1 receptor
  • the chimeric Fab fragment of 3H7 (heavy chain)
  • the chimeric Fab fragment of 3H7 (light chain)
KeywordsMEMBRANE 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 endothelial cell apoptotic process / regulation of establishment or maintenance of cell polarity / regulation of vascular permeability / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of Rho protein signal transduction ...Tie signaling pathway / glomerulus vasculature development / regulation of endothelial cell apoptotic process / regulation of establishment or maintenance of cell polarity / regulation of vascular permeability / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of Rho protein signal transduction / microvillus / positive regulation of Rac protein signal transduction / positive regulation of intracellular signal transduction / positive regulation of focal adhesion assembly / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / negative regulation of angiogenesis / cellular response to mechanical stimulus / receptor protein-tyrosine kinase / negative regulation of inflammatory response / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / signaling receptor activity / heart development / RAF/MAP kinase cascade / angiogenesis / basolateral plasma membrane / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / receptor complex / positive regulation of MAPK cascade / ciliary basal body / apical plasma membrane / membrane raft / focal adhesion / centrosome / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain ...Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsKim, H.M. / Jo, G.H. / Hong, H.J. / Han, A.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other governmentInstitute for Basic Science, IBS-R030-C1 Korea, Republic Of
Other governmentInstitute for Basic Science, IBS-R025-D1 Korea, Republic Of
CitationJournal: 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
DepositionFeb 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: the chimeric Fab fragment of 3H7 (heavy chain)
B: the chimeric Fab fragment of 3H7 (light chain)
C: the chimeric Fab fragment of 3H7 (heavy chain)
D: the chimeric Fab fragment of 3H7 (light chain)
E: Angiopoietin-1 receptor
F: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,43140
Polymers140,3206
Non-polymers2,11034
Water13,277737
1
A: the chimeric Fab fragment of 3H7 (heavy chain)
B: the chimeric Fab fragment of 3H7 (light chain)
E: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,52625
Polymers70,1603
Non-polymers1,36522
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: the chimeric Fab fragment of 3H7 (heavy chain)
D: the chimeric Fab fragment of 3H7 (light chain)
F: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,90515
Polymers70,1603
Non-polymers74512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.080, 77.340, 121.849
Angle α, β, γ (deg.)103.820, 96.890, 90.590
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody the chimeric Fab fragment of 3H7 (heavy chain)


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 the chimeric Fab fragment of 3H7 (light chain)


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 Angiopoietin-1 receptor / Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and ...Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and EGF homology domains-2 / Tyrosine-protein kinase receptor TEK / Tyrosine-protein kinase receptor TIE-2 / hTIE2 / p140 TEK


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 / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X8M, 5MYA

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
RfactorNum. reflection% reflection
Rfree0.2331 2006 2.36 %
Rwork0.1826 82923 -
obs0.1838 84929 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.41 Å2 / Biso mean: 39.2863 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: final / Resolution: 2.094→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 340 737 10698
Biso mean--45.99 36.27 -
Num. residues----1256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0944-2.14670.29421420.2385572487
2.1467-2.20480.26811340.2232594292
2.2048-2.26970.26221510.2223593691
2.2697-2.34290.2761370.2174564487
2.3429-2.42670.25031530.2124594292
2.4267-2.52380.25611410.2074610293
2.5238-2.63870.29751450.2115606893
2.6387-2.77770.28331410.2072591691
2.7777-2.95180.25011420.203574589
2.9518-3.17960.24561440.1956609994
3.1796-3.49950.26621460.1749605493
3.4995-4.00560.19721430.1619580189
4.0056-5.04550.18381440.1354608993
Refinement TLS params.Method: refined / Origin x: 34.9749 Å / Origin y: 15.1799 Å / Origin z: 89.5922 Å
111213212223313233
T0.4037 Å20.0146 Å2-0.0101 Å2-0.157 Å20.0044 Å2--0.198 Å2
L0.0531 °20.0193 °20.0347 °2--0.2301 °20.0526 °2--0.3836 °2
S-0.0054 Å °0.0082 Å °-0.0003 Å °0.0012 Å °-0.0027 Å °0.0421 Å °0.0055 Å °0.04 Å °0.0021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 321
2X-RAY DIFFRACTION1allB1 - 214
3X-RAY DIFFRACTION1allC1 - 311
4X-RAY DIFFRACTION1allD1 - 214
5X-RAY DIFFRACTION1allE540 - 801
6X-RAY DIFFRACTION1allF540 - 801
7X-RAY DIFFRACTION1allG1 - 737

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