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- PDB-4k0v: Structural basis for angiopoietin-1 mediated signaling initiation -

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Basic information

Entry
Database: PDB / ID: 4k0v
TitleStructural basis for angiopoietin-1 mediated signaling initiation
Components
  • Angiopoietin-1
  • TEK tyrosine kinase variant
KeywordsSIGNALING PROTEIN/TRANSFERASE / cellular signaling / Tie receptor tyrosine kinase / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


brain-derived neurotrophic factor receptor activity / platelet-derived growth factor beta-receptor activity / boss receptor activity / placental growth factor receptor activity / platelet-derived growth factor alpha-receptor activity / heparin proteoglycan biosynthetic process / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / macrophage colony-stimulating factor receptor activity ...brain-derived neurotrophic factor receptor activity / platelet-derived growth factor beta-receptor activity / boss receptor activity / placental growth factor receptor activity / platelet-derived growth factor alpha-receptor activity / heparin proteoglycan biosynthetic process / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / macrophage colony-stimulating factor receptor activity / activation of transmembrane receptor protein tyrosine kinase activity / regulation of establishment or maintenance of cell polarity / protein tyrosine kinase collagen receptor activity / positive regulation of coagulation / transmembrane receptor protein kinase activity / negative regulation of vascular endothelial growth factor signaling pathway / stem cell factor receptor activity / regulation of endothelial cell apoptotic process / regulation of skeletal muscle satellite cell proliferation / insulin-like growth factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / hepatocyte growth factor receptor activity / circulatory system development / vascular endothelial growth factor receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / endothelial cell proliferation / heart trabecula formation / fibroblast growth factor receptor activity / definitive hemopoiesis / negative regulation of cell adhesion / insulin receptor activity / regulation of vascular permeability / protein localization to cell surface / sprouting angiogenesis / negative regulation of vascular permeability / epidermal growth factor receptor activity / positive regulation of Rac protein signal transduction / positive chemotaxis / positive regulation of Rho protein signal transduction / negative regulation of endothelial cell apoptotic process / microvillus / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / substrate adhesion-dependent cell spreading / positive regulation of endothelial cell proliferation / Tie2 Signaling / negative regulation of angiogenesis / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / positive regulation of protein ubiquitination / cellular response to mechanical stimulus / negative regulation of inflammatory response / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / blood coagulation / positive regulation of angiogenesis / heart development / cell-cell junction / cell-cell signaling / angiogenesis / RAF/MAP kinase cascade / signaling receptor activity / extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / basolateral plasma membrane / cytoskeleton / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell differentiation / protein kinase activity / signaling receptor complex / cell surface receptor signaling pathway / apical plasma membrane / membrane raft / receptor ligand activity / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / : / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / ANG-1-like domain / Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Fibrinogen alpha chain / Laminin-type EGF domain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain ...: / ANG-1-like domain / Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Fibrinogen alpha chain / Laminin-type EGF domain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Epidermal growth factor-like domain. / Fibronectin type III domain / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / Fibronectin type 3 domain / EGF-like 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 / 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 / Angiopoietin-1 / receptor protein-tyrosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.51 Å
AuthorsYu, X. / Seegar, T.C.M. / Dalton, A.C. / Tzvetkova-Robev, D. / Goldgur, Y. / Nikolov, D.B. / Barton, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for angiopoietin-1-mediated signaling initiation.
Authors: Yu, X. / Seegar, T.C. / Dalton, A.C. / Tzvetkova-Robev, D. / Goldgur, Y. / Rajashankar, K.R. / Nikolov, D.B. / Barton, W.A.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TEK tyrosine kinase variant
B: Angiopoietin-1


Theoretical massNumber of molelcules
Total (without water)85,2102
Polymers85,2102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.533, 189.533, 334.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TEK tyrosine kinase variant


Mass: 58896.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q59HG2, UniProt: Q02763*PLUS
#2: Protein Angiopoietin-1 / ANG-1


Mass: 26313.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPT1, KIAA0003 / Cell line (production host): HEK 293 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15389
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.51→30.012 Å / Num. all: 18336 / Num. obs: 18062 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Redundancy: 5.5 % / Rsym value: 0.14 / Net I/σ(I): 17.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GY7

2gy7


Resolution: 4.51→30.012 Å / SU ML: 0.53 / σ(F): 0 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 517 3.03 %
Rwork0.2484 --
obs0.2496 17061 93.08 %
all-18336 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.6528 Å20 Å2-0 Å2
2--18.6528 Å20 Å2
3----37.3055 Å2
Refinement stepCycle: LAST / Resolution: 4.51→30.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 0 0 5775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115949
X-RAY DIFFRACTIONf_angle_d1.6258033
X-RAY DIFFRACTIONf_dihedral_angle_d18.6332189
X-RAY DIFFRACTIONf_chiral_restr0.109833
X-RAY DIFFRACTIONf_plane_restr0.0081054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.51-4.96010.30351240.24413784X-RAY DIFFRACTION87
4.9601-5.67360.27551230.23724041X-RAY DIFFRACTION92
5.6736-7.13220.36541300.2914222X-RAY DIFFRACTION95
7.1322-30.01230.25811400.23674497X-RAY DIFFRACTION98

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