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- PDB-6zbr: VEGF-A 13:107 crystallized with 4C bicyclic peptide -

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Basic information

Entry
Database: PDB / ID: 6zbr
TitleVEGF-A 13:107 crystallized with 4C bicyclic peptide
Components
  • Chains: P
  • Vascular endothelial growth factor A
KeywordsPEPTIDE BINDING PROTEIN / growth factor / peptide ligand / lactam bridge / alpha-helix stabilization / SIGNALING PROTEIN
Function / homology
Function and homology information


basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / 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 / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / motor neuron migration / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / activation of protein kinase activity / chemoattractant activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / secretory granule / kidney development / cytokine activity / positive regulation of epithelial cell proliferation
Similarity search - Function
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 / Cystine-knot cytokine
Similarity search - Domain/homology
PHOSPHATE ION / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 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 1.2Jan 24, 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)24,8969
Polymers24,2103
Non-polymers6866
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Kd 4C-peptide:VEGF= 156mM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-76 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.075, 55.603, 77.073
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

#1: Protein/peptide Chains: P


Mass: 1952.254 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(+) / Cell line (production host): Rosetta2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15692
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: Diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (VEGF)2:2 PEPTIDE_4C 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: 1.6→55.6 Å / Num. obs: 31383 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 21.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.027 / Rrim(I) all: 0.082 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4517 / CC1/2: 0.966 / Rpim(I) all: 0.246 / Rrim(I) all: 0.726 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHENIX1.18-3855phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLT

1flt


Resolution: 1.6→45.09 Å / SU ML: 0.1921 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 1594 5.11 %
Rwork0.2036 29613 -
obs0.2054 31207 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 45 145 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011776
X-RAY DIFFRACTIONf_angle_d1.26472403
X-RAY DIFFRACTIONf_chiral_restr0.0618247
X-RAY DIFFRACTIONf_plane_restr0.0078311
X-RAY DIFFRACTIONf_dihedral_angle_d20.4847690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.34671430.32522637X-RAY DIFFRACTION99.18
1.65-1.710.33861460.29322627X-RAY DIFFRACTION99.32
1.71-1.780.32311410.26432641X-RAY DIFFRACTION99.43
1.78-1.860.27181420.22972675X-RAY DIFFRACTION99.65
1.86-1.960.24311310.21962657X-RAY DIFFRACTION99.29
1.96-2.080.23631410.19882685X-RAY DIFFRACTION99.65
2.08-2.240.21961560.19672658X-RAY DIFFRACTION99.61
2.24-2.470.23361480.19482698X-RAY DIFFRACTION99.61
2.47-2.820.25411590.20062701X-RAY DIFFRACTION99.83
2.82-3.560.25151550.19432728X-RAY DIFFRACTION99.72
3.56-45.090.20831320.18952906X-RAY DIFFRACTION99.87
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)
10.05657967609320.076389750519-0.02983049973020.0713985597739-0.04541775839780.01032557562260.0435348295138-0.02637637353490.1976281695430.159069491238-0.0785144638808-0.132026057166-0.3320414652680.119430636715-0.04082392151961.68975762598-0.08151977360570.03082052173750.455915284813-0.01175644160290.6709585912427.90906296242.93382467661.15728104338
20.250503848143-0.0321052510869-0.008803721508740.01526180332990.01916448826960.02964125325320.1294034014260.1215578876880.253692264133-0.122636646978-0.0975874467513-0.04914339668490.0782000235816-0.2013785327010.03073888526871.898801784360.3153354521180.066244479248-0.151575918865-0.3320581305360.38499754340425.061739363846.4721683571-7.57902523135
30.1753906751750.114404530859-0.01955698975770.864888481192-0.07058790630440.119779015911-0.03660166693160.2247043668620.109193889043-0.378566029636-0.1717036785190.433317882445-0.492747185895-0.4194974287550.01094207745790.2030261269630.0206654996456-0.01302279757680.267716173819-0.02967969052850.33674645622421.39457736316.957860893068.07633775611
40.4801467939460.2754641447490.06331672468111.216093172630.8716117897820.8015945217710.212989284378-0.304867431647-0.08995637381020.599786920601-0.52488642564-0.559139250856-0.1039338382360.241216258376-0.1497496858660.164602429805-0.0269394928935-0.04872026704570.2303144014710.07079183572730.30530240984431.185568257821.9453101156-6.96633418222
50.356444172826-0.601486297133-0.193199319550.8302546709810.0667475508410.5900911507610.0423383464667-0.002574398006620.01393629868480.125446780391-0.152556376834-0.4497953843860.1730211730610.261172179435-0.06218331504710.1965571897380.00241541205703-0.0373087432460.2883306093420.03711945419570.29625432541733.958089713422.2827387978-8.82032325919
60.517905321138-0.3538279979020.05839717258310.319374818049-0.418577637850.8402984944260.09584611425750.0433620006010.0919684852331-0.307077194332-0.20592094526-0.04151797648330.04703456483220.208923393792.90029612747E-70.236142809842-0.002522521350480.01437618293840.2558475638270.02169826244330.22024342667131.53157882526.8948147127-14.3887513637
7-0.04798813081830.05947999568310.1336439211880.0406859971263-0.005627580971690.746681899007-0.006194985174290.0532248163830.0062719056378-0.07585949192820.08660493756390.1129114288090.283116186811-0.06132234402880.002690317976610.2179421564460.00842368484096-0.003853149015020.212335754669-0.005504699112780.22545492773528.925081494216.9335419757-13.234424606
80.1267569928220.260081720089-0.09419618532161.11711631782-0.6292931959380.508393502270.00538856073728-0.1969357637850.1386222699210.576759156317-0.1657173323850.526947484647-0.0742907462821-0.753421866640.02231314619340.2710415188040.01223391298440.01679117828520.284614378568-0.03775238643150.3158454895423.096911360232.9969253085-7.8357901936
90.327894356665-0.296222467292-0.2154863559860.7968004580031.112581554231.69380620307-0.04941402313180.153685700720.146208144187-0.2150136305560.393519594914-0.170250907067-0.5789615988230.8035314452780.1779138721710.1918407536120.00981224893183-0.01835331744880.36612172733-0.06639767306660.21594498827631.228178062216.39149129266.2578126712
100.2030702206830.235092651042-0.2554322199730.581385436347-0.4010695630510.349089919329-0.245525918467-0.120211339671-0.636246552103-0.0233849295439-0.46201714725-0.194796883507-0.262027721845-0.290755015567-0.0325266633290.4069519304150.0682738547805-0.04816032310660.747945399697-0.2863179402310.73463985269640.70309770996.360265260413.9521543695
110.1401754082560.08112970432670.1571947467380.06098824831850.1481013257520.397147322534-0.1222472993290.08503744645720.0461991034887-0.2978720574570.1770522553840.0594299546593-0.1617189300110.1617545533621.41953948533E-70.2647111627190.012739614074-0.001962530418590.272644836755-0.009395953912470.19208922192329.776877556711.94869687617.97188416771
120.01948993160640.003011958182-0.00658305983220.0117952749141-0.0029362839567-0.003123342690320.1018332210320.3471933765680.08687630245360.0292202067666-0.02854395859820.148584192243-0.453371963443-0.226925036677-4.43391877226E-50.537637782502-0.117539069808-0.01000407929010.3813553859090.04499584273330.26425514835135.252720550435.5754428006-0.828369664018
130.2547523251690.169088317898-0.0339135930730.1372081502370.1563625772290.652732276786-0.00792836200573-0.06363132508590.003381949524050.0569495440770.03125365945030.04485052878060.01597250085730.2785001586024.61939423886E-70.319840174522-0.001405757009440.01308096673180.234934885591-0.0004395295069960.22619293509229.101694853817.23024091213.4073479768
140.00579931275595-0.00434215198623-0.0149987335065-0.001738366318470.01195361001750.0147227568829-0.2231218142630.211956850290.09564789514640.00694029605491-0.759920720040.0989672954436-0.246023647329-0.320463610475-4.09931126691E-50.5081548258410.0436183170758-0.1942828596450.5868001002730.1221000989340.5703102445535.4238497755-7.73329021614.7998691361
150.128977993041-0.06185159341350.002569248212231.05950617388-0.08295449419080.494196578907-0.0417320051992-0.0726230672097-0.01314485412130.03048110075360.0957191581980.176476741853-0.2979449206680.1918107480560.04015155677030.362662211864-0.02210409810550.01206827931330.245778048468-0.002446546916040.21505026048229.908387384121.274493855313.0087482519
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'P' and (resid 1 through 8 )PA1 - 81 - 8
22chain 'P' and (resid 9 through 14 )PA9 - 149 - 14
33chain 'V' and (resid 13 through 26 )VB13 - 261 - 14
44chain 'V' and (resid 27 through 38 )VB27 - 3815 - 26
55chain 'V' and (resid 39 through 65 )VB39 - 6527 - 53
66chain 'V' and (resid 66 through 89 )VB66 - 8954 - 78
77chain 'V' and (resid 90 through 107 )VB90 - 10779 - 100
88chain 'W' and (resid 13 through 26 )WC13 - 261 - 14
99chain 'W' and (resid 27 through 38 )WC27 - 3815 - 26
1010chain 'W' and (resid 39 through 45 )WC39 - 4527 - 33
1111chain 'W' and (resid 46 through 58 )WC46 - 5834 - 46
1212chain 'W' and (resid 59 through 65 )WC59 - 6547 - 53
1313chain 'W' and (resid 66 through 83 )WC66 - 8354 - 73
1414chain 'W' and (resid 84 through 89 )WC84 - 8974 - 79
1515chain 'W' and (resid 90 through 107 )WC90 - 10780 - 97

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