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- PDB-9ivt: Crystal structure of Ang1 receptor-binding domain -

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Basic information

Entry
Database: PDB / ID: 9ivt
TitleCrystal structure of Ang1 receptor-binding domain
ComponentsAngiopoietin-1
KeywordsCELL ADHESION / Angiopoietin-1
Function / homology
Function and homology information


regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin proteoglycan biosynthetic process / negative regulation of vascular endothelial growth factor signaling pathway / regulation of skeletal muscle satellite cell proliferation / positive regulation of coagulation / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion ...regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin proteoglycan biosynthetic process / negative regulation of vascular endothelial growth factor signaling pathway / regulation of skeletal muscle satellite cell proliferation / positive regulation of coagulation / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion / regulation of tumor necrosis factor production / negative regulation of vascular permeability / protein localization to cell surface / regulation of canonical NF-kappaB signal transduction / activation of transmembrane receptor protein tyrosine kinase activity / sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein import into nucleus / positive chemotaxis / cell-substrate adhesion / hemopoiesis / microvillus / positive regulation of receptor internalization / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / positive regulation of endothelial cell migration / positive regulation of cell adhesion / positive regulation of protein ubiquitination / receptor tyrosine kinase binding / blood coagulation / RAF/MAP kinase cascade / : / neuron apoptotic process / angiogenesis / negative regulation of neuron apoptotic process / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor ligand activity / membrane raft / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Fibrinogen alpha chain / 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.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, R. / Huang, M.D. / Jiang, L.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82070142 China
CitationJournal: Sci Adv / Year: 2025
Title: Development of a recombinant Ang1 variant with enhanced Tie2 binding and its application to attenuate sepsis in mice.
Authors: Wang, R. / Li, H. / Xie, Z. / Huang, M. / Xu, P. / Yuan, C. / Li, J. / Flaumenhaft, R. / Huang, M. / Jiang, L.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiopoietin-1


Theoretical massNumber of molelcules
Total (without water)26,1881
Polymers26,1881
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.600, 61.980, 44.550
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21A-641-

HOH

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Components

#1: Protein Angiopoietin-1 / ANG-1


Mass: 26188.311 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): HEK293 / Production host: Mammalia (mammals) / References: UniProt: Q15389
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 38.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3.5 M Sodium formate at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→24.05 Å / Num. obs: 21020 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1093 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→24.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.003 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1089 5.2 %RANDOM
Rwork0.177 ---
obs0.179 19930 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å2-1.62 Å2
2---0.7 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 142 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131819
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181616
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6432453
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5893716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7925217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6122.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36415300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1451510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1512.05871
X-RAY DIFFRACTIONr_mcbond_other2.152.049870
X-RAY DIFFRACTIONr_mcangle_it3.3013.0671087
X-RAY DIFFRACTIONr_mcangle_other3.2993.0681088
X-RAY DIFFRACTIONr_scbond_it2.8762.342946
X-RAY DIFFRACTIONr_scbond_other2.8742.341946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4593.3961365
X-RAY DIFFRACTIONr_long_range_B_refined7.06625.0542145
X-RAY DIFFRACTIONr_long_range_B_other6.96224.7482122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 85 -
Rwork0.26 1466 -
obs--99.68 %

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