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

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Basic information

Entry
Database: PDB / ID: 4jyo
TitleStructural basis for angiopoietin-1 mediated signaling initiation
ComponentsAngiopoietin-1
KeywordsSIGNALING PROTEIN / cellular signaling / Tie receptor tyrosine kinase
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 biosynthetic process / regulation of skeletal muscle satellite cell proliferation / negative regulation of cytokine production involved in immune response / regulation of tumor necrosis factor production / negative regulation of cell adhesion / negative regulation of vascular permeability ...regulation of macrophage migration inhibitory factor signaling pathway / Tie signaling pathway / glomerulus vasculature development / positive regulation of blood-brain barrier permeability / heparin biosynthetic process / regulation of skeletal muscle satellite cell proliferation / negative regulation of cytokine production involved in immune response / regulation of tumor necrosis factor production / negative regulation of cell adhesion / negative regulation of vascular permeability / protein localization to cell surface / regulation of canonical NF-kappaB signal transduction / sprouting angiogenesis / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of protein import into nucleus / positive chemotaxis / cell-substrate adhesion / microvillus / positive regulation of receptor internalization / hemopoiesis / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / positive regulation of endothelial cell migration / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / receptor tyrosine kinase binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / RAF/MAP kinase cascade / angiogenesis / neuron apoptotic process / collagen-containing extracellular matrix / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / 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
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionMar 31, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Angiopoietin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3542
Polymers26,3141
Non-polymers401
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Angiopoietin-1
hetero molecules

X: Angiopoietin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7084
Polymers52,6272
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area1520 Å2
ΔGint-35 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.968, 80.968, 187.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: 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 / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15389
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Na/K-tartate, 0.1 M Tris, 0.2 M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING 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 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→70.12 Å / Num. all: 13340 / Num. obs: 13192 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.079 / Net I/σ(I): 24.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Num. unique all: 1279 / Rsym value: 0.42 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z3S

1z3s


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.341 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24231 649 4.9 %RANDOM
Rwork0.18637 ---
obs0.18894 12559 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.277 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.01 Å20 Å2
2--2.02 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 1 88 1843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211810
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9152441
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3215216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77323.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6681510
X-RAY DIFFRACTIONr_chiral_restr0.1390.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211427
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.181.51067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18821695
X-RAY DIFFRACTIONr_scbond_it3.3973743
X-RAY DIFFRACTIONr_scangle_it5.2334.5746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 51 -
Rwork0.25 896 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 18.716 Å / Origin y: -1.056 Å / Origin z: -18.318 Å
111213212223313233
T0.0135 Å2-0.03 Å20.0005 Å2-0.5233 Å2-0.0102 Å2--0.0273 Å2
L1.5333 °20.0342 °2-0.6812 °2-1.6295 °20.2361 °2--1.2508 °2
S-0.0965 Å °0.1429 Å °-0.0531 Å °-0.0546 Å °0.1031 Å °-0.1166 Å °-0.0143 Å °0.1489 Å °-0.0066 Å °

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