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- PDB-5utk: Crystal structure of the membrane proximal three fibronectin type... -

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Basic information

Entry
Database: PDB / ID: 5utk
TitleCrystal structure of the membrane proximal three fibronectin type III (FNIII) domains of Tie2 (Tie2[FNIIIa-c])
ComponentsAngiopoietin-1 receptor
KeywordsTRANSFERASE / receptor tyrosine kinase / extracellular region / dimerization / fibronectin type III domain
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 / growth factor binding / positive regulation of Rac protein signal transduction / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / negative regulation of endothelial cell apoptotic process / cell surface receptor protein tyrosine kinase signaling pathway / Tie2 Signaling / response to cAMP / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / negative regulation of angiogenesis / substrate adhesion-dependent cell spreading / basal plasma membrane / receptor protein-tyrosine kinase / response to peptide hormone / negative regulation of inflammatory response / 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 / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / response to hypoxia / protein kinase activity / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / focal adhesion / 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. / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / : / 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. / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / : / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMoore, J.O. / Lemmon, M.A. / Ferguson, K.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R03-CA187021 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM099891 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM107435 United States
American Cancer Society123704-PF-13-034-01-DMC United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Dimerization of Tie2 mediated by its membrane-proximal FNIII domains.
Authors: Moore, J.O. / Lemmon, M.A. / Ferguson, K.M.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Angiopoietin-1 receptor
B: Angiopoietin-1 receptor


Theoretical massNumber of molelcules
Total (without water)68,2742
Polymers68,2742
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-2 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.950, 52.026, 111.427
Angle α, β, γ (deg.)90.000, 117.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: 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: 34136.977 Da / Num. of mol.: 2 / Fragment: unp residues 399-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q02763, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 3.3 Å3/Da / Density % sol: 62.77 % / Description: Three-dimensional plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25-40% glycerol, 2.5-15% PEG 3K, 100 mM sodium acetate, 100 mM sodium phosphate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.04, 0.97944, 0.97927, 0.94928
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.041
20.979441
30.979271
40.949281
ReflectionResolution: 2.5→50 Å / Num. obs: 30201 / % possible obs: 97.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.549 / Net I/σ(I): 9.2 / Num. measured all: 95446
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.572.30.56221741.019185.1
2.57-2.662.70.47124231.06194.9
2.66-2.753.30.4325381.222199.6
2.75-2.863.40.33625741.326199.5
2.86-2.993.40.2725261.391199.6
2.99-3.153.30.19825561.583199.3
3.15-3.353.30.15225381.72198.8
3.35-3.613.30.1225451.88198.4
3.61-3.973.20.09725591.888198.7
3.97-4.543.20.07825481.831198.8
4.54-5.723.20.06925901.653198.9
5.72-503.20.06526301.619197.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→49.328 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1539 5.1 %
Rwork0.2254 28626 -
obs0.2266 30165 96.59 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.36 Å2 / Biso mean: 59.7567 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.5→49.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4415 0 0 77 4492
Biso mean---54.03 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054523
X-RAY DIFFRACTIONf_angle_d0.9016202
X-RAY DIFFRACTIONf_chiral_restr0.056720
X-RAY DIFFRACTIONf_plane_restr0.004809
X-RAY DIFFRACTIONf_dihedral_angle_d13.6721630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.58070.33371090.31582096220578
2.5807-2.6730.38211310.29512504263594
2.673-2.780.30661450.29082685283099
2.78-2.90650.33681430.27782631277499
2.9065-3.05970.30621490.26262655280499
3.0597-3.25140.28551240.24692703282799
3.2514-3.50240.2371330.23232639277299
3.5024-3.85470.23911370.21882640277798
3.8547-4.41220.23551500.2032665281599
4.4122-5.55770.20971620.17812683284599
5.5577-49.33750.19681560.21172725288197

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