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- PDB-3s1b: The Development of Peptide-based Tools for the Analysis of Angiog... -

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Basic information

Entry
Database: PDB / ID: 3s1b
TitleThe Development of Peptide-based Tools for the Analysis of Angiogenesis
Components
  • Vascular endothelial growth factor A
  • mini-Z
KeywordsSIGNALING PROTEIN / VEGF / cystine knot / mini-Z
Function / homology
Function and homology information


Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / post-embryonic camera-type eye development ...Signaling by VEGF / basophil chemotaxis / lymph vessel morphogenesis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / : / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor 1 binding / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of mast cell chemotaxis / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / motor neuron migration / eye photoreceptor cell development / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / mammary gland alveolus development / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor-2 signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of axon extension involved in axon guidance / camera-type eye morphogenesis / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / retinal ganglion cell axon guidance / induction of positive chemotaxis / vascular wound healing / positive regulation of protein autophosphorylation / dopaminergic neuron differentiation / positive regulation of epithelial tube formation / neuropilin binding / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / tube formation / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of leukocyte migration / cell migration involved in sprouting angiogenesis / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / artery morphogenesis / cardiac muscle cell development / branching involved in blood vessel morphogenesis / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / sprouting angiogenesis / platelet-derived growth factor receptor binding / extracellular matrix binding / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of neuroblast proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / vascular endothelial growth factor signaling pathway / positive chemotaxis / positive regulation of sprouting angiogenesis / mesoderm development / ovarian follicle development / chemoattractant activity / cell maturation / outflow tract morphogenesis / lung development / vasculogenesis / macrophage differentiation / fibronectin binding / monocyte differentiation / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / heart morphogenesis / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / lactation / kidney development / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / in utero embryonic development / positive regulation of epithelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of cell adhesion / negative regulation of miRNA transcription / secretory granule / platelet alpha granule lumen / cytokine activity / VEGFR2 mediated cell proliferation / growth factor activity / adherens junction / positive regulation of protein-containing complex assembly
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. ...Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding domain / Vascular endothelial growth factor A, long form-like domain / : / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMurray, J.M. / Wiesmann, C.
CitationJournal: Chem.Biol. / Year: 2011
Title: The development of Peptide-based tools for the analysis of angiogenesis.
Authors: Fedorova, A. / Zobel, K. / Gill, H.S. / Ogasawara, A. / Flores, J.E. / Tinianow, J.N. / Vanderbilt, A.N. / Wu, P. / Meng, Y.G. / Williams, S.P. / Wiesmann, C. / Murray, J. / Marik, J. / Deshayes, K.
History
DepositionMay 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Vascular endothelial growth factor A
A: mini-Z


Theoretical massNumber of molelcules
Total (without water)15,2582
Polymers15,2582
Non-polymers00
Water00
1
V: Vascular endothelial growth factor A
A: mini-Z

V: Vascular endothelial growth factor A
A: mini-Z


Theoretical massNumber of molelcules
Total (without water)30,5154
Polymers30,5154
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4370 Å2
ΔGint-39 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 70.940, 161.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11266.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGF, VEGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Protein/peptide mini-Z


Mass: 3990.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: fmoc solid-phase peptide synthesis
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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M NaOAc, 0.02 M CaCl2, MPD 30.0% v/v, pH 6.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLEx-ray1
2SINGLEx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6 % / Number: 38151 / Rmerge(I) obs: 0.115 / Χ2: 1 / D res high: 2.8 Å / D res low: 20 Å / Num. obs: 6381 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.982098.510.0470.7715.6
4.775.9897.910.0730.8915.8
4.174.7798.510.0821.1626.1
3.794.1799.110.1231.1226.1
3.523.7999.110.1531.2336.3
3.323.5298.610.2121.0826.3
3.153.3298.210.2891.0226.3
3.023.1598.610.4050.9056.3
2.93.0298.710.5540.8475.9
2.82.996.910.7660.9445.1
ReflectionResolution: 2.8→20 Å / Num. obs: 6381 / % possible obs: 98 % / Redundancy: 6 % / Rsym value: 0.079

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7801 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 272 4.74 %RANDOM
Rwork0.2207 ---
obs0.2224 5733 98.64 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.474 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso max: 198.07 Å2 / Biso mean: 65.6861 Å2 / Biso min: 26.28 Å2
Baniso -1Baniso -2Baniso -3
1-9.5493 Å2-0 Å2-0 Å2
2--9.5493 Å20 Å2
3----19.0986 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 0 0 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071084
X-RAY DIFFRACTIONf_angle_d0.9891455
X-RAY DIFFRACTIONf_chiral_restr0.053155
X-RAY DIFFRACTIONf_plane_restr0.003192
X-RAY DIFFRACTIONf_dihedral_angle_d17.699420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-3.65340.33031300.26632632276298
3.6534-40.46240.22211420.20232829297199
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11980.1067-0.09040.0914-0.08590.0650.232-0.14910.58640.0218-0.22720.2742-0.1566-0.07640.371-0.14720.00180.2418-0.01280.2898-27.5777-25.033918.917
20.57570.6167-0.07771.5960.19530.5580.1478-0.04840.1450.2831-0.1868-0.001-0.4360.21960.243-0.0192-0.01620.2534-0.06030.2237-24.24763.63997.1739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:34A1 - 34
2X-RAY DIFFRACTION2chain V and resid 13:107V13 - 107

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