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- PDB-3s1k: The Development of Peptide-based Tools for the Analysis of Angiog... -

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Basic information

Entry
Database: PDB / ID: 3s1k
TitleThe Development of Peptide-based Tools for the Analysis of Angiogenesis
Components
  • Vascular endothelial growth factor A
  • Z-domain
KeywordsSIGNALING PROTEIN / VEGF / cystine knot / Z-domain / phage-display / cystine-knot
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 / VEGF-activated neuropilin signaling pathway / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor 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 / positive regulation of axon extension involved in axon guidance / endothelial cell chemotaxis / camera-type eye morphogenesis / positive regulation of protein localization to early endosome / positive regulation of trophoblast cell migration / surfactant homeostasis / positive regulation of protein autophosphorylation / retinal ganglion cell axon guidance / induction of positive chemotaxis / vascular wound healing / dopaminergic neuron differentiation / positive regulation of epithelial tube formation / transmembrane receptor protein tyrosine kinase activator activity / 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 / positive regulation of vascular endothelial growth factor signaling pathway / branching involved in blood vessel morphogenesis / 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 / outflow tract morphogenesis / chemoattractant activity / mesoderm development / macrophage differentiation / fibronectin binding / monocyte differentiation / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / lung development / heart morphogenesis / vasculogenesis / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / ovarian follicle development / positive regulation of blood vessel endothelial cell migration / cell maturation / lactation / kidney development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / epithelial cell differentiation / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / positive regulation of cell adhesion / positive regulation of epithelial cell proliferation / secretory granule / platelet alpha granule lumen / cytokine activity / VEGFR2 mediated cell proliferation / growth factor activity / adherens junction / in utero embryonic development / positive regulation of protein-containing complex assembly
Similarity search - Function
Vascular endothelial growth factor A, long form-like domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 A, long form-like domain / Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 / Immunoglobulin FC, subunit C / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Up-down Bundle / Mainly Beta / Mainly Alpha
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: 2.55 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 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
A: Z-domain
B: Z-domain
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,2424
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-47 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.228, 72.760, 76.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Z-domain


Mass: 6672.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Fmoc solid-phase peptide synthesis
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11948.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: vegf / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M KI, 0.1 M MES, PEG 4000 25.0% v/v, pH 6.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→52.706 Å / Num. all: 14337 / Num. obs: 14337 / % possible obs: 91.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.534.90.5571.41101822300.557100
2.53-2.684.90.4671.7842417080.46780.1
2.68-2.874.90.282.7939719210.2895.9
2.87-3.14.80.1794.2902018600.17999.8
3.1-3.394.80.1066.6819517100.10699.8
3.39-3.794.80.0798.2524110970.07969.4
3.79-4.384.60.05710.5530911620.05783.1
4.38-5.374.20.04413.2483811490.04496.3
5.37-7.594.80.0698.445669420.06999.3
7.59-52.7064.60.03115.625395580.03198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXdev_751refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.918 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7681 / SU ML: 0.7 / σ(F): 1.39 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 632 4.87 %Random
Rwork0.2266 ---
obs0.2288 12982 99.23 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.967 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 152.2 Å2 / Biso mean: 56.9583 Å2 / Biso min: 17.84 Å2
Baniso -1Baniso -2Baniso -3
1--9.0168 Å20 Å20 Å2
2--7.6865 Å2-0 Å2
3---1.3303 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 37 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042404
X-RAY DIFFRACTIONf_angle_d0.7853241
X-RAY DIFFRACTIONf_chiral_restr0.053346
X-RAY DIFFRACTIONf_plane_restr0.004431
X-RAY DIFFRACTIONf_dihedral_angle_d17.443911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5501-2.7470.33991280.31812412254099
2.747-3.02340.36871100.287824612571100
3.0234-3.46070.32821260.252524622588100
3.4607-4.35930.26321240.20862432255698
4.3593-41.92320.21441440.186825832727100
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.21562.4133-0.69974.10310.4053.49040.4567-0.1322-0.7571-0.0559-0.5755-0.17690.85440.4634-0.33871.24820.11350.19580.1921-0.10110.5348-11.2979-38.5589-7.493
27.07420.7901-0.78364.37491.30974.13740.1869-0.7936-0.7620.5362-0.4935-0.06441.62930.2646-0.10051.07540.05410.15310.34410.01910.697-14.9533-37.6831.729
36.56871.00320.74734.76540.61254.2825-0.19050.5485-1.50050.08580.122-0.21181.06810.4817-0.21381.57510.1430.16980.38880.03230.7974-13.233-46.9787-3.6233
44.125-2.4752-1.18735.75240.19092.3226-0.1446-0.02090.3236-0.2581-0.0039-0.4041-0.020.2052-0.05620.4408-0.0677-0.0020.1661-0.0030.2201-12.77179.08318.9883
56.153-1.5620.08975.12871.75233.820.3976-0.58390.3372-0.67320.1782-0.3263-0.0706-0.3762-0.08560.653-0.08470.01690.27510.02570.2186-12.28768.54989.0301
65.4575-1.8218-0.15684.17140.60313.38040.21660.07610.6313-0.236-0.0202-0.3572-0.63530.1664-0.26920.6562-0.05960.13490.18130.05810.3945-10.871517.520215.3876
72.08960.27340.4422.13392.67776.4502-0.1716-0.1678-0.1862-0.07720.2061-0.0813-0.0993-0.11120.08340.4277-0.0196-0.01480.15810.0350.227-17.4804-8.60346.0645
84.14423.01691.81332.41160.76642.1982-0.11481.1124-1.5279-1.7435-0.02181.29651.1644-0.1362-0.33881.1111-0.0301-0.4276-0.1504-0.09680.9819-28.3557-25.0762-15.3196
91.5315-0.26521.23615.85210.44624.26580.0346-0.1545-0.1364-0.22060.03610.09860.0734-1.12880.11240.511-0.11660.10860.19810.13440.1776-21.468-12.5731-1.7789
101.7197-0.91770.24523.9529-0.86363.0473-0.02670.6972-0.4002-0.7144-0.08080.16120.0613-0.17090.10660.55690.01320.01160.20060.14290.038-17.685-14.3148-9.3731
113.298-1.29380.72784.9518-0.41084.73530.2210.3041-0.574-0.4167-0.10090.19190.7215-0.0705-0.00980.4978-0.04380.03950.36080.05570.2415-19.8212-17.4925-10.3621
120.3941-0.8709-1.19592.95072.47394.41830.011-0.072-0.45620.2314-0.31190.08020.61830.06040.28070.64090.0060.0610.18860.01210.4034-18.2667-19.86363.4202
134.101-1.2482-0.5653.6795-1.14440.6129-0.7636-1.46810.58990.9605-0.61781.22690.0141-1.13430.41290.54020.0986-0.15490.4143-0.10860.5429-34.244-1.255517.8129
140.658-1.6454-1.03365.79523.04653.6663-0.11960.1305-0.35250.2793-0.55460.57480.9227-0.61940.38990.6915-0.17610.10760.22060.02680.2778-24.2203-15.74978.2828
150.48230.6455-0.11326.113.15172.66120.14340.0407-0.25011.3629-0.6280.00571.1763-0.3530.40890.7546-0.09890.04860.19190.02660.268-23.3187-12.376917.6445
161.34610.48280.43943.52214.0534.433-0.6459-0.9253-0.5255-0.3784-0.71120.55170.7567-0.379-0.01420.6157-0.2270.01940.21670.1454-0.1322-25.099-9.132517.5058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:23)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:37)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 38:57)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:23)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 24:37)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 38:57)B0
7X-RAY DIFFRACTION7chain 'V' and (resseq 13:38)V0
8X-RAY DIFFRACTION8chain 'V' and (resseq 39:45)V0
9X-RAY DIFFRACTION9chain 'V' and (resseq 46:65)V0
10X-RAY DIFFRACTION10chain 'V' and (resseq 66:83)V0
11X-RAY DIFFRACTION11chain 'V' and (resseq 84:107)V0
12X-RAY DIFFRACTION12chain 'W' and (resseq 14:38)W0
13X-RAY DIFFRACTION13chain 'W' and (resseq 39:45)W0
14X-RAY DIFFRACTION14chain 'W' and (resseq 46:66)W0
15X-RAY DIFFRACTION15chain 'W' and (resseq 67:83)W0
16X-RAY DIFFRACTION16chain 'W' and (resseq 84:106)W0

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