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- PDB-5n06: Crystal structure of Tie1 Fibronectin-like domain 3 -

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Basic information

Entry
Database: PDB / ID: 5n06
TitleCrystal structure of Tie1 Fibronectin-like domain 3
ComponentsTyrosine-protein kinase receptor Tie-1
KeywordsSIGNALING PROTEIN / receptor / fibronectin-like domains / heterodimerization
Function / homology
Function and homology information


branching involved in lymph vessel morphogenesis / plasma membrane fusion / lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / regulation of extracellular matrix assembly / tissue remodeling / multicellular organism development / positive regulation of kinase activity / aortic valve morphogenesis / plasma membrane => GO:0005886 ...branching involved in lymph vessel morphogenesis / plasma membrane fusion / lymphatic endothelial cell differentiation / regulation of endothelial cell proliferation / regulation of extracellular matrix assembly / tissue remodeling / multicellular organism development / positive regulation of kinase activity / aortic valve morphogenesis / plasma membrane => GO:0005886 / mesoderm development / vasculogenesis / response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / negative regulation of cell migration / receptor protein-tyrosine kinase / positive regulation of angiogenesis / angiogenesis / in utero embryonic development / receptor complex / signal transduction / ATP binding
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. ...Immunoglobulin / Immunoglobulin domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulin-like domain superfamily / 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
Tyrosine-protein kinase receptor Tie-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsLeppanen, V.-M. / Saharinen, P. / Alitalo, K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization.
Authors: Leppanen, V.M. / Saharinen, P. / Alitalo, K.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 1, 2024Group: 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: Tyrosine-protein kinase receptor Tie-1
B: Tyrosine-protein kinase receptor Tie-1


Theoretical massNumber of molelcules
Total (without water)28,1342
Polymers28,1342
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-16 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.054, 54.054, 107.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tyrosine-protein kinase receptor Tie-1


Mass: 14066.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence includes N-terminal Mellitin signal peptide, cloning artefect (ADP) and C-terminal His-tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: TIE1, TIE
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: P35590, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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 Å3/Da / Density % sol: 37 % / Description: Hexagonal rods
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris buffer at pH 8.0 - 9.0 and 18-24% PEG 8000 (w/v)
PH range: 8.0 - 9.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liguid nitrogen cooling system
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 6161 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 79.9 Å2 / Rsym value: 0.078 / Net I/σ(I): 15.2
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 951 / Rsym value: 0.935 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Tie2 Fn3 domain

Resolution: 2.501→28.416 Å / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 33.97
Details: Maximum likelihood refinement of XYZ coordinates, TLS parameters and individual B-factors. Twin law: k, h, -l. Twin fraction 0.510.
RfactorNum. reflection% reflectionSelection details
Rfree0.3151 370 6.01 %Random selection
Rwork0.2435 ---
obs0.2489 6161 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 107.6 Å2
Refinement stepCycle: LAST / Resolution: 2.501→28.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 0 73 1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051374
X-RAY DIFFRACTIONf_angle_d0.7871889
X-RAY DIFFRACTIONf_dihedral_angle_d11.656471
X-RAY DIFFRACTIONf_chiral_restr0.028221
X-RAY DIFFRACTIONf_plane_restr0.004243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5022-2.8640.32691230.32111924X-RAY DIFFRACTION94
2.864-3.60720.34021230.28261918X-RAY DIFFRACTION94
3.6072-28.41740.30621240.21891939X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0925-0.33064.95367.74970.58652.0736-1.2161-0.0317-1.7636-0.07240.99910.09321.29132.8104-0.01970.92310.31130.11871.6295-0.1361.09148.2116-19.0932.543
24.9125-1.7980.81113.17810.67743.37360.77071.2248-1.91760.82070.65781.3730.2194-0.3429-0.64380.8911.40731.06882.130.61881.6832-6.5935-18.2148-5.7205
32.07241.4377.0832.0434-2.7372.01431.9042-0.5914-0.9720.6187-0.41540.4520.3491-0.7413-1.51570.6455-0.00660.05331.0919-0.03420.57510.0604-12.78044.0302
44.88491.3963-2.5693.84784.69349.83521.1129-1.6351-0.76590.26421.4578-1.0382-0.3807-1.8986-2.33750.66710.0214-0.00120.98440.21351.03272.8949-10.339911.0151
54.7469-1.9371-3.19017.25712.06442.0155-0.2390.09210.6035-0.38361.6507-1.1351-0.827-0.2518-1.46140.625-0.2020.04050.999300.73134.3904-13.0099-4.391
62.2893-5.19045.62265.2362-2.5967.0201-1.7618-0.46320.76061.54361.1314-0.2964-1.39120.5410.6230.91720.1561-0.06721.00980.04610.64252.4028-12.95776.3958
70.7175-1.82011.15382.04240.65363.8070.0049-0.51990.119-0.39060.01071.8418-1.46840.5862-0.17771.30220.13660.02190.94810.11141.1695-14.999515.3818-9.24
83.7343-1.59130.63088.07165.5738.05870.19810.42890.7168-0.7536-0.43681.2125-1.983-0.10980.26991.01410.1192-0.22870.70440.00891.0415-17.375313.2731-2.0007
92.01936.53254.01612.1165-6.30337.88592.79942.05411.4762-2.4577-0.2952-0.7293-0.89423.0441-1.8281.46-0.03470.62171.373-0.22041.1551-5.861820.193-4.0448
109.32081.466-2.89226.2972-2.82824.7671.42110.63280.23220.7259-0.57882.3172-1.4747-1.274-0.54740.92970.20310.2060.8309-0.02230.8277-18.98253.45334.7733
112.0211-1.23821.9042.0321-6.62732.02480.0271.62111.3974-0.84390.34872.4698-1.27750.2569-0.05551.2181-0.1167-0.07720.96580.3011.0857-10.8496.6669-6.4084
124.10420.2599-0.15783.13550.25720.87550.2591.31780.69950.60820.51970.0352-0.3049-0.4081-0.76671.28640.77710.3511.74180.2941.0114-6.83526.438-8.9623
134.80750.2698-1.28327.0422-0.63762.71011.5438-1.62371.02781.32-1.0343-0.293-0.23290.8166-0.42811.6938-0.2833-0.13790.9415-0.30661.0356-8.51429.78863.4782
141.9559-3.6632-1.06151.74850.8530.51071.34722.21412.4114-0.60652.13371.435-2.43360.0483-2.65373.1027-1.4744-0.38862.78610.52340.9735-4.690219.0911-13.1438
153.7329-0.33890.82822.93590.87230.5172-1.30591.34540.9099-0.5544-0.1807-0.5494-0.6977-0.55331.21062.34550.2299-0.0080.7479-0.15310.463-14.54987.6024-6.924
163.2218-0.43720.38365.6641.32380.44231.1213-0.829-1.4575-0.0414-1.53780.02950.42831.04670.15710.79030.3272-0.01952.02190.42760.92740.2692-17.67627.0749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 644 through 663 )
2X-RAY DIFFRACTION2chain 'A' and (resid 664 through 675 )
3X-RAY DIFFRACTION3chain 'A' and (resid 676 through 681 )
4X-RAY DIFFRACTION4chain 'A' and (resid 682 through 695 )
5X-RAY DIFFRACTION5chain 'A' and (resid 696 through 705 )
6X-RAY DIFFRACTION6chain 'A' and (resid 706 through 726 )
7X-RAY DIFFRACTION7chain 'A' and (resid 727 through 738 )
8X-RAY DIFFRACTION8chain 'B' and (resid 644 through 655 )
9X-RAY DIFFRACTION9chain 'B' and (resid 656 through 663 )
10X-RAY DIFFRACTION10chain 'B' and (resid 664 through 675 )
11X-RAY DIFFRACTION11chain 'B' and (resid 676 through 682 )
12X-RAY DIFFRACTION12chain 'B' and (resid 683 through 695 )
13X-RAY DIFFRACTION13chain 'B' and (resid 696 through 705 )
14X-RAY DIFFRACTION14chain 'B' and (resid 706 through 714 )
15X-RAY DIFFRACTION15chain 'B' and (resid 715 through 721 )
16X-RAY DIFFRACTION16chain 'B' and (resid 722 through 737 )

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