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- PDB-9lv4: Cryo-EM Structure of Human Tie2/minibinder tw1102_4 helices Complex -

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Basic information

Entry
Database: PDB / ID: 9lv4
TitleCryo-EM Structure of Human Tie2/minibinder tw1102_4 helices Complex
Components
  • Angiopoietin-1 receptor
  • Minibinder tw1102
KeywordsDE NOVO PROTEIN / artificial designed minibinder / TEK tyrosine kinase / angiopoietin receptor / endothelial cells.
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 / protein kinase activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / apical plasma membrane / ciliary basal body / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsFu, Y. / Kim, H.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: Designed Tie2-specific minibinder with therapeutic potential
Authors: Fu, Y. / Kim, H.M.
History
DepositionFeb 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Angiopoietin-1 receptor
A: Minibinder tw1102


Theoretical massNumber of molelcules
Total (without water)61,9012
Polymers61,9012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 47921.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligand binding domain of human Tie2 / Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q02763, receptor protein-tyrosine kinase
#2: Protein Minibinder tw1102


Mass: 13978.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: artificial designed minibinder protein / Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hTie2/minibinder tw1102_4 helix complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2200 mMsodium chlorideNaCl1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 10mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: CDS mode is used
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 77160 X / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13517

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2PHENIX1.16_3549:model refinement
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1206082
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 589066 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 2GY5

2gy5


Pdb chain-ID: A / Accession code: 2GY5 / Chain residue range: 23-445 / Details: hTie2 LBD domain / Pdb chain residue range: 23-445 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063620
ELECTRON MICROSCOPYf_angle_d0.8284869
ELECTRON MICROSCOPYf_dihedral_angle_d3.9432202
ELECTRON MICROSCOPYf_chiral_restr0.053529
ELECTRON MICROSCOPYf_plane_restr0.005623

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