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- PDB-6zcd: VEGF-A 13:107 crystallized with 1C bicyclic peptide -

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Basic information

Entry
Database: PDB / ID: 6zcd
TitleVEGF-A 13:107 crystallized with 1C bicyclic peptide
Components
  • Derived from V114 peptide
  • 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 / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / negative regulation of adherens junction organization / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / regulation of nitric oxide mediated signal transduction / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lymphangiogenesis / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of axon extension involved in axon guidance / lung vasculature development / vascular wound healing / eye photoreceptor cell development / regulation of hematopoietic progenitor cell differentiation / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / camera-type eye morphogenesis / positive regulation of protein autophosphorylation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neuropilin binding / positive regulation of branching involved in ureteric bud morphogenesis / induction of positive chemotaxis / coronary artery morphogenesis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / commissural neuron axon guidance / positive regulation of vascular permeability / vascular endothelial growth factor receptor 2 binding / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / surfactant homeostasis / platelet-derived growth factor receptor binding / retinal ganglion cell axon guidance / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / extracellular matrix binding / endothelial cell proliferation / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cardiac muscle cell development / positive regulation of endothelial cell chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of cell migration involved in sprouting angiogenesis / artery morphogenesis / vascular endothelial growth factor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / fibronectin binding / positive regulation of cell division / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / ovarian follicle development / cell maturation / lactation / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / extracellular matrix / positive regulation of endothelial cell migration
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: 1.8 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 10, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Derived from V114 peptide
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8829
Polymers24,1963
Non-polymers6866
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Kd VEGF:peptide 1C = 38nM in hepes/NaOH 50mM pH 7.5 NaCl 150mM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-74 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.644, 55.699, 77.210
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 Derived from V114 peptide


Mass: 1938.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DERIVED FROM V114 PEPTIDE FROM GENENTECH INC.; CG of ASP 14 and NZ of LYS 10 covalently linked by lactam bridge;
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P15692
#3: Chemical
ChemComp-MPD / (4S)-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


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


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (VEGF)2:2 PEPTIDE_1C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 13.5MG/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: 1.8→53.64 Å / Num. obs: 22094 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.107 / Χ2: 0.94 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1271 / CC1/2: 0.957 / Rpim(I) all: 0.419 / Rrim(I) all: 0.951 / Χ2: 0.76 / % 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: 1.8→45.17 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1127 5.14 %
Rwork0.1899 20819 -
obs0.1924 21946 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 45 124 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011781
X-RAY DIFFRACTIONf_angle_d1.14172408
X-RAY DIFFRACTIONf_chiral_restr0.0629247
X-RAY DIFFRACTIONf_plane_restr0.0071313
X-RAY DIFFRACTIONf_dihedral_angle_d20.0496687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.34751360.29342533X-RAY DIFFRACTION99.44
1.88-1.980.29671420.25072565X-RAY DIFFRACTION99.23
1.98-2.110.25811400.20962545X-RAY DIFFRACTION99.59
2.11-2.270.26071400.19492586X-RAY DIFFRACTION99.74
2.27-2.50.21791390.18972580X-RAY DIFFRACTION99.31
2.5-2.860.27651530.19852598X-RAY DIFFRACTION99.85
2.86-3.60.2591520.18062608X-RAY DIFFRACTION99.14
3.6-45.170.19031250.1682804X-RAY DIFFRACTION99.93
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)
15.303324042360.63523265238-5.158564990795.90039908263-1.068240391245.04849332713-0.1492436938460.287799532559-0.00557581299887-0.253174694182-0.1799505001290.657313253388-0.20107467819-0.8089246003680.3023952491010.3811800783490.00410739738414-0.03802667363770.27711814397-0.02991824514720.30097847925821.16799441956.951366186038.05202862445
24.863609678425.00831476032-4.910978153645.1552907764-5.03664085755.015044487770.303362152678-0.383574296321-0.4104411615210.86101399529-0.494426759307-0.684364676174-0.2348625419380.1713151741560.2846513065710.446569769601-0.0221854190137-0.0239956665120.2202491217310.02553761070220.26954392988330.998259523322.0063808867-6.99147110945
31.014435725871.3620060094-0.9910542169869.19088607882-3.579931809113.65699063127-0.0224663916239-0.0537695558858-0.162029527177-0.0988984506458-0.38856888814-0.9256290518650.3672900599790.4539704410260.4354953663320.3451921915070.0480784224586-0.02072554456580.3163955540080.02952633017670.2654401154733.418082714320.1517920309-7.85758231221
40.8872354240670.632479576335-0.6152624095118.09291369005-3.115001959323.573881342160.09307692482050.03206719779380.00140025931665-0.381562465025-0.248756105241-0.2396877369770.005656475505040.235345590.1677482570730.3452283012480.02695639346070.009161282964310.235387384010.02812651440150.16918778230430.509329625326.8281062217-15.0391764036
53.66943449214-2.57997262801-3.062275956094.127409730970.01584175533374.53518462970.1515227382460.178194208617-0.419531545057-0.315031210519-0.299897760182-0.01412356385062.165718797220.57475372903-0.1062984284780.8337371174490.1014763479610.008595620480530.354824521107-0.01513284138920.31116851643829.02000288914.63791484497-9.59928517604
68.412493807281.732479313375.743338226246.372216714321.883674221754.53524716927-0.149938450136-0.2696413065640.1325035557950.328253773594-0.1162550191330.507730345086-0.406540634393-1.043845189120.3319214820650.3845962037370.02846755314760.0655958384170.256790640856-0.04808998586110.26988900134722.812801429833.0526514186-7.79638975616
77.50553888161-5.78575109835.308166766279.68580610891-6.249625562958.762962069020.1763437379930.4736378018130.00370348671844-0.270929347245-0.17675933046-0.0734230312896-0.07481612410280.8723179870410.05624140534110.416198307914-0.04209474934850.06427905717530.319805781023-0.04646322011010.19383417445331.019836535616.18238390116.24324739462
88.705464921061.39864875143-5.46438798951.57356124436-3.445322585938.3144764371-0.7948949867850.283963839133-0.773497895915-0.725165804801-0.4371047154470.6485735230460.878868896626-0.7019437234350.527188672860.7179579290790.102729080441-0.09904468206980.881843203631-0.4644041621080.73114558147340.33957371996.1764937159714.1756710733
91.0299632774-0.8880246319390.3824238925713.11160506059-3.519110685084.629129304220.07541420893460.05968954090430.177222547765-0.0865726518383-0.170159126405-0.270200788322-0.3797160620070.3829506165930.1222076838320.399757798149-0.01433192181630.02968416291560.296006288050.003670058058180.18743164846431.280540905119.70042639175.13788816749
102.314025242711.67311956647-0.6563943189274.242418698570.02731371188482.77829901730.0511051498441-0.0556501215317-0.2399733836610.3551138727840.00426934369001-0.2338166054570.2014809262470.506121020845-0.05415665440720.4150846204650.053248059624-0.04377274786430.327010730693-0.006891077908430.18855300163730.864501561911.935563404313.8042922482
111.164828546560.94992097895-0.3462676717814.22854966707-3.986289005264.60330216030.0760711783911-0.09075043097470.08534838681860.305438842668-0.008189134945780.176963369346-0.3704662365770.343515058429-0.01096958801240.390840212044-0.01644949517910.01668069728070.294820543308-0.03063075131350.18741247713229.643030904519.74313892613.1572726326
128.11214560038-4.711603303613.998568237147.24605000633-3.347840920579.30271839809-0.1630538556320.4154572004971.73200070073-0.576419757433-0.576417381919-0.714713050809-2.96078504132-0.1914679564080.78482275541.44064428885-0.007660361245870.08422154245840.587215091954-0.05062595130740.65622646943727.436484301843.00181015781.00138870767
133.754177867371.28852738283-2.245983998490.442132258402-0.7709479293951.34347828483-0.2671956812350.7010144927562.180482564870.3035533406980.0791135228290.502578094856-3.154230240790.002775688048620.2663173050591.718689266580.0496811151182-0.3706477885550.6272892647160.08851089830540.82277151401224.479933613146.3040843586-8.21855185435
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 )VB13 - 261 - 14
22chain 'V' and (resid 27 through 38 )VB27 - 3815 - 26
33chain 'V' and (resid 39 through 65 )VB39 - 6527 - 56
44chain 'V' and (resid 66 through 99 )VB66 - 9957 - 90
55chain 'V' and (resid 100 through 107 )VB100 - 10791 - 98
66chain 'W' and (resid 13 through 26 )WC13 - 261 - 14
77chain 'W' and (resid 27 through 38 )WC27 - 3815 - 26
88chain 'W' and (resid 39 through 45 )WC39 - 4527 - 33
99chain 'W' and (resid 46 through 65 )WC46 - 6534 - 53
1010chain 'W' and (resid 66 through 88 )WC66 - 8854 - 78
1111chain 'W' and (resid 89 through 107 )WC89 - 10779 - 97
1212chain 'P' and (resid 1 through 8 )PA1 - 81 - 8
1313chain 'P' and (resid 9 through 15 )PA9 - 159 - 15

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