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- PDB-6z3f: VEGF-A 13:107 crystallized with 2C bicyclic peptide -

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Basic information

Entry
Database: PDB / ID: 6z3f
TitleVEGF-A 13:107 crystallized with 2C bicyclic peptide
Components
  • Chains: P
  • Vascular endothelial growth factor A
KeywordsPEPTIDE BINDING PROTEIN / growth factor / peptide ligand / lactam bridge / alpha-helix stabilization
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 cytokine
Similarity search - Domain/homology
ACETIC ACID / AMINO GROUP / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGaucher, J.-F. / Broussy, S. / Reille-Seroussi, M.
CitationJournal: Chemistry / Year: 2022
Title: Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands.
Authors: Gaucher, J.F. / Reille-Seroussi, M. / Broussy, S.
History
DepositionMay 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Chains: P
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,62810
Polymers24,1943
Non-polymers4347
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Kd(VEGF:peptide 2C)= 60mM in hepes/NaOH 50mM NaCl 150mM pH 7.5
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-48 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.419, 55.824, 77.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide / Protein , 2 types, 3 molecules PVW

#1: Protein/peptide Chains: P


Mass: 1936.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: derived from V114 peptide - genentech Inc. / Source: (synth.) synthetic construct (others)
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11128.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: PET22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta2 / References: UniProt: P15692

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Non-polymers , 4 types, 97 molecules

#3: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.55 % / Description: diamond plate shape 300 * 300um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (VEGF)2:2 PEPTIDE_3C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 / MPD 35% (V/V) / (NH4)2PO4 150MM

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.272 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.272 Å / Relative weight: 1
ReflectionResolution: 2.1→45.31 Å / Num. obs: 14341 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.71 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.05 / Rrim(I) all: 0.141 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8871 / Rpim(I) all: 0.267 / Rrim(I) all: 0.748 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
MxCuBE1.18_3855data collection
XDS1.18_3855data reduction
SCALAdata scaling
PHENIX1.18_3855phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FLT1

Resolution: 2.1→44.55 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 735 5.17 %
Rwork0.2096 13484 -
obs0.2122 14219 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 29 90 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221732
X-RAY DIFFRACTIONf_angle_d0.52922331
X-RAY DIFFRACTIONf_chiral_restr0.0437239
X-RAY DIFFRACTIONf_plane_restr0.0034310
X-RAY DIFFRACTIONf_dihedral_angle_d18.5631663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.33081500.27342629X-RAY DIFFRACTION99.29
2.26-2.490.29091420.23642640X-RAY DIFFRACTION98.9
2.49-2.850.26361580.22532642X-RAY DIFFRACTION98.97
2.85-3.590.31971530.20722709X-RAY DIFFRACTION99.58
3.59-44.550.21241320.18782864X-RAY DIFFRACTION99.57
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)
17.779861477460.138602250987-5.456136715725.840823774910.9223297110634.04665971278-0.1251787977660.02994072616240.0958070441875-0.30877716108-0.5314113732620.666509202854-0.690693890073-0.7728262060060.4527513268150.368213275772-0.00882077456334-0.03534896529240.251429197957-0.02055673237950.31730805049621.52049643666.991639089168.15682087965
20.7291908274940.502941960271-0.6629750900559.56310265287-1.934725468512.51578135-0.0440853554629-0.040411617423-0.0579648299830.0469722490182-0.205916100816-0.876218434783-0.09686570482060.3283121809620.246818207560.3738515632050.039648890884-0.02573471931680.2790891254030.006232748724570.29497724590632.741590715123.8103229313-10.6674381454
31.055660980281.26678231579-0.554377720258.58505380644-0.6810116984791.90968055203-0.2063414384340.0441130412022-0.260963692266-0.6811474308220.336945499352-0.1819150271950.772515348783-0.1390981506880.01771476508320.574115828140.01893097998080.01099174486520.247322049685-0.0354681825820.24433299274129.153955845117.2850310868-13.3406518497
44.157806549620.001384722566344.13170740725.947129631680.2087157457684.69514355020.100041943544-0.3732985121860.4388746311460.428863623464-0.2899797970260.793269643174-0.555977088562-1.527896850.09506267015760.3738967143590.008656096692320.07317569084290.38238807335-0.04976390463930.35631179721523.177274553633.0160254825-7.92867511828
57.71782191883-4.85197099502-0.2944628263223.174015638540.3142337251036.98994730265-0.575527374808-0.4430785095240.179090577167-0.3997965433890.767758633527-0.54312489044-0.1622968027331.09567664904-0.2388242562940.342346806602-0.011187027918-0.001627354918510.347248477626-0.06202777212860.32081382908331.478692640416.35508248776.28401557938
65.176644664832.4487829354-4.217870218551.85360301679-3.207794873735.49858173266-0.8655536029870.0185706609264-1.27828421765-1.64666889194-0.9651897066430.707835713853-0.629967443302-1.633637776611.236194865620.7772437758060.0177830954554-0.1433094278340.839549529121-0.5453962827921.1157624430440.91760785326.2841447862314.1905597623
71.77178913724-0.5891512611970.3798807240078.1220601005-1.726189518323.25273435854-0.03118225024920.3071931517510.18188746413-0.1619898678850.0581169388401-0.260301140447-0.5602087074620.5615762120940.006054410142430.517845743366-0.01697259667670.02792175546190.375328417878-0.02792428631620.18608306085131.695487950319.72462937085.1732558845
81.223465260450.916164782949-0.7304401609114.96640293985-0.6555141837822.9832102457-0.0234861646163-0.053788929481-0.01136022587550.226136524945-0.016100998462-0.03019578838690.2945252164690.4287921176540.02821427105880.5500671773080.0191075745634-0.003826274936570.335948811328-0.009300698109790.2108546577629.430667518317.864755976913.4492562706
92.408068093961.55108305306-0.3007861687717.13100526196-3.329865862625.414862551470.2635890731490.172697581045-1.24753338803-0.45533457087-1.23063208459-2.209819249051.66358556482.674199352991.103271194411.072954188250.447707729239-0.24304629021.149913851420.102611520531.4141937505335.9951028017-7.4129004274115.3282777342
100.6167164166790.032938179786-0.5038141670717.30738056656-3.417159479154.408861706210.0332312543192-0.08734451273850.1887179439410.9291342386240.152133443651-0.00218390334257-0.7314253561420.434185402209-0.1409518249290.626574870523-0.0153294283591-0.02884121811050.366007851485-0.01622221036320.23597594960430.098393623121.363897644213.1319390946
117.24475645868-0.9667204177740.5438796050135.95129587673-1.640576317595.24432987351-0.524163193996-0.2006308803361.206891247750.6288764593580.763035150828-0.311333633899-1.61319896737-0.427485540769-0.1895466827371.204970841450.1048416589910.1105866295250.541247689571-0.009303758109520.63212647639727.938527723543.10099732360.998210293879
129.1356349153.15919590564-3.569155118618.226542987540.7198576353753.43352716660.1840657740510.6990529105261.63150196523-1.091390974860.6207502574870.812277194232-0.469617891006-0.122666963504-0.7816610061191.04280696357-0.0134277660802-0.146983714540.4260645509570.1186871408930.59848047599424.900898877546.375465314-8.68297781185
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'V' and (resid 13 through 26 )VC13 - 261 - 14
22chain 'V' and (resid 27 through 89 )VC27 - 8915 - 77
33chain 'V' and (resid 90 through 107 )VC90 - 10778 - 95
44chain 'W' and (resid 13 through 26 )WD13 - 261 - 14
55chain 'W' and (resid 27 through 38 )WD27 - 3815 - 26
66chain 'W' and (resid 39 through 45 )WD39 - 4527 - 33
77chain 'W' and (resid 46 through 65 )WD46 - 6534 - 53
88chain 'W' and (resid 66 through 83 )WD66 - 8354 - 71
99chain 'W' and (resid 84 through 89 )WD84 - 8972 - 77
1010chain 'W' and (resid 90 through 107 )WD90 - 10778 - 95
1111chain 'P' and (resid 1 through 8 )PA1 - 81 - 8
1212chain 'P' and (resid 9 through 15 )PA - B9 - 159

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