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- PDB-5myb: Homodimerization of Tie2 Fibronectin-like domains 2 and 3 in spac... -

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Basic information

Entry
Database: PDB / ID: 5myb
TitleHomodimerization of Tie2 Fibronectin-like domains 2 and 3 in space group P21
ComponentsAngiopoietin-1 receptor
KeywordsSIGNALING PROTEIN / receptor / fibronectin-like domains / dimerization / homotypic interactions
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 / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / response to cAMP / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / transmembrane receptor protein tyrosine kinase activity / 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / response to hypoxia / protein kinase activity / phosphorylation / 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 / Fibronectin type 3 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / 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 / 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: 2.6 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
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0628
Polymers75,1672
Non-polymers1,8966
Water1,11762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint19 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.460, 48.490, 80.670
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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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: 37583.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn- ...Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn-like domain was not in the crystals apparently due to proteolytic removal prior crystallization.
Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q02763, receptor protein-tyrosine kinase
#2: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: rod-like
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris buffer at pH 7.0 - 8.5 and 14-20% PEG 3350 (w/v)
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling system
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 104.1 Å2
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.873 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYSTAL STRUCTURE OF TIE2 FN-LIKE DOMAINS IN SPACE GROUP C2

Resolution: 2.6→39.8 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.66
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1053 6 %Random selction in XDS
Rwork0.222 ---
obs0.225 17549 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 123 62 3123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073128
X-RAY DIFFRACTIONf_angle_d1.2714292
X-RAY DIFFRACTIONf_dihedral_angle_d14.4131115
X-RAY DIFFRACTIONf_chiral_restr0.071524
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.71840.34091290.34232005X-RAY DIFFRACTION97
2.7184-2.86170.37941290.3252045X-RAY DIFFRACTION99
2.8617-3.04090.36761310.31222036X-RAY DIFFRACTION99
3.0409-3.27560.36571310.27022058X-RAY DIFFRACTION99
3.2756-3.6050.29211310.24862043X-RAY DIFFRACTION99
3.605-4.12620.33621330.2392084X-RAY DIFFRACTION99
4.1262-5.19680.25731330.1882083X-RAY DIFFRACTION99
5.1968-39.79990.23531360.19962142X-RAY DIFFRACTION99
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)
18.09780.5113-1.95355.5643-2.27096.72890.1002-0.33410.10171.0718-0.1334-0.0447-0.06410.04430.01380.8567-0.0146-0.08790.5228-0.00790.7272-10.3239-8.339437.317
22.76133.1519-2.14725.3995-2.62133.104-0.13190.3202-0.029-1.03370.29670.71710.5349-0.2022-0.15290.69570.1502-0.06220.983-0.00420.85596.3818-3.929416.347
36.75512.4322-2.14456.3757-2.32583.88490.26640.47340.2977-0.11450.09090.1992-0.3331-0.0304-0.33260.81150.10740.04611.11910.02130.819315.51989.405413.8131
44.8496-0.1010.66043.887-0.2116.20780.24461.0778-0.3255-1.17310.10980.71640.5631-0.9656-0.33141.0861-0.084-0.24381.07560.16620.892252.8465-14.007711.1752
56.4736-1.70530.2025.0325-0.71916.31370.2146-0.0531-0.407-0.36340.10580.43521.3145-0.5234-0.3130.9606-0.1389-0.17020.71430.0870.780455.3202-13.832720.5235
63.7954-1.0038-1.60020.33120.8493.2715-0.1861-1.30670.34020.72410.38830.11470.0136-0.7813-0.17070.78480.0427-0.02731.7420.02990.896837.27211.600632.43
73.3453-1.28570.80549.0512-1.79462.11910.0254-0.88080.99250.3822-0.1704-0.6193-0.5522-0.11390.10730.8921-0.02520.03121.2894-0.19861.002129.012912.468826.2522
84.8323-3.4007-1.92429.84521.5862.2517-0.3624-2.10150.94631.59180.3682-0.2407-0.4069-0.0701-0.00420.94630.0505-0.08771.6954-0.32961.085726.158615.27429.4006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 543 THROUGH 632 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 633 THROUGH 645 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 646 THROUGH 734 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 542 THROUGH 574 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 575 THROUGH 632 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 633 THROUGH 645 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 646 THROUGH 695 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 696 THROUGH 734 )

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