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- EMDB-63412: Cryo-EM Structure of Human Tie2/minibinder tw1102_4 helices Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63412
TitleCryo-EM Structure of Human Tie2/minibinder tw1102_4 helices Complex
Map datamain map
Sample
  • Complex: hTie2/minibinder tw1102_4 helix complex
    • Protein or peptide: Angiopoietin-1 receptor
    • Protein or peptide: Minibinder tw1102
Keywordsartificial designed minibinder / TEK tyrosine kinase / angiopoietin receptor / endothelial cells. / DE NOVO PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsFu Y / Kim HM
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: Designed Tie2-specific minibinder with therapeutic potential
Authors: Fu Y / Kim HM
History
DepositionFeb 11, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63412.png

Downloads & links

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Map

FileDownload / File: emd_63412.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 248.832 Å		0.65 Å/pix.
x 384 pix.
= 248.832 Å		0.65 Å/pix.
x 384 pix.
= 248.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.238
Minimum - Maximum-0.85907316 - 1.3870126
Average (Standard dev.)-0.0016703694 (±0.018607982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 248.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A map

Fileemd_63412_half_map_1.map
Annotationhalf A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_63412_half_map_2.map
Annotationhalf B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hTie2/minibinder tw1102_4 helix complex

EntireName: hTie2/minibinder tw1102_4 helix complex
Components
  • Complex: hTie2/minibinder tw1102_4 helix complex
    • Protein or peptide: Angiopoietin-1 receptor
    • Protein or peptide: Minibinder tw1102

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Supramolecule #1: hTie2/minibinder tw1102_4 helix complex

SupramoleculeName: hTie2/minibinder tw1102_4 helix complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Angiopoietin-1 receptor

MacromoleculeName: Angiopoietin-1 receptor / type: protein_or_peptide / ID: 1 / Details: ligand binding domain of human Tie2 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.921996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AMDLILINSL PLVSDAETSL TCIASGWRPH EPITIGRDFE ALMNQHQDPL EVTQDVTREW AKKVVWKREK ASKINGAYFC EGRVRGEAI RIRTMKMRQQ ASFLPATLTM TVDKGDNVNI SFKKVLIKEE DAVIYKNGSF IHSVPRHEVP DILEVHLPHA Q PQDAGVYS ...String:
AMDLILINSL PLVSDAETSL TCIASGWRPH EPITIGRDFE ALMNQHQDPL EVTQDVTREW AKKVVWKREK ASKINGAYFC EGRVRGEAI RIRTMKMRQQ ASFLPATLTM TVDKGDNVNI SFKKVLIKEE DAVIYKNGSF IHSVPRHEVP DILEVHLPHA Q PQDAGVYS ARYIGGNLFT SAFTRLIVRR CEAQKWGPEC NHLCTACMNN GVCHEDTGEC ICPPGFMGRT CEKACELHTF GR TCKERCS GQEGCKSYVF CLPDPYGCSC ATGWKGLQCN EACHPGFYGP DCKLRCSCNN GEMCDRFQGC LCSPGWQGLQ CER EGIPRM TPKIVDLPDH IEVNSGKFNP ICKASGWPLP TNEEMTLVKP DGTVLHPKDF NHTDHFSVAI FTIHRILPPD SGVW VCSVN TVAGMVEKPF NISVKVLPKP LNAPN

UniProtKB: Angiopoietin-1 receptor

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Macromolecule #2: Minibinder tw1102

MacromoleculeName: Minibinder tw1102 / type: protein_or_peptide / ID: 2 / Details: artificial designed minibinder protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.978975 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSGSEEEQKL VEEAIEKLTK ILEELAKKYG EKMKEPKEYY LRMSEKIKKN EQPEQDMAIL IHNAGKEVLK LTGDEEAALE LAKLSAKLF QYAGDTDGAV RALKQSGIGE EAEKIAEEIR KKAAGS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Details: 10mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeTFS KRIOS
DetailsCDS mode is used
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13517 / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 77160 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1206082
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2gy5


Details: hTie2 ligand binding domian (2GY5) is used as an initial model. The structure of minibinder tw1102 is manually built using AlphaFold3-predicted structure as reference.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 589066
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2gy5


Chain - Chain ID: A / Chain - Residue range: 23-445 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: hTie2 LBD domain
RefinementSpace: REAL
Output model

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

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