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- PDB-6zfl: High resolution structure of VEGF-A 12:107 crystallized in tetrag... -

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Basic information

Entry
Database: PDB / ID: 6zfl
TitleHigh resolution structure of VEGF-A 12:107 crystallized in tetragonal form
ComponentsVascular endothelial growth factor A
KeywordsSIGNALING PROTEIN / growth factor
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 / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding ...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 / negative regulation of adherens junction organization / 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 blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / 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 / regulation of nitric oxide mediated signal transduction / positive regulation of protein localization to early endosome / eye photoreceptor cell development / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of vascular permeability / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / endothelial cell proliferation / extracellular matrix binding / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / positive regulation of protein autophosphorylation / monocyte differentiation / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / mammary gland alveolus development / neuroblast proliferation / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / cell maturation / ovarian follicle development / homeostasis of number of cells within a tissue / positive regulation of endothelial cell proliferation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / 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)
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 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 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 1.3Oct 23, 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
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2789
Polymers22,5202
Non-polymers7587
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-60 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.340, 88.340, 40.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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


Mass: 11260.030 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
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.51 Å3/Da / Density % sol: 64.93 % / Description: elongated rode 20 x 20 x 200um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: (VEGF)2:2 PEPTIDE_2C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. (SEE ID 6Z3F) mix 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : TRIS/HCL 100MM PH 8.5 / MPD 42% (V/V) / (NH4)2PO4 200MM

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Data collection

DiffractionMean temperature: 100 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→44.17 Å / Num. obs: 41413 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6017 / CC1/2: 0.707 / Rpim(I) all: 0.464 / Rrim(I) all: 0.838 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
MxCuBEdata collection
SCALAdata scaling
PHENIX1.18_3855phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLT

1flt


Resolution: 1.6→44.17 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 2069 5 %
Rwork0.1641 39283 -
obs0.1652 41352 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.99 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 47 208 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951703
X-RAY DIFFRACTIONf_angle_d1.02312319
X-RAY DIFFRACTIONf_chiral_restr0.0605242
X-RAY DIFFRACTIONf_plane_restr0.0069304
X-RAY DIFFRACTIONf_dihedral_angle_d18.1176681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28671350.26242583X-RAY DIFFRACTION99.31
1.64-1.680.30231130.2512623X-RAY DIFFRACTION99.45
1.68-1.720.23581550.24152572X-RAY DIFFRACTION99.53
1.72-1.770.26921260.2112642X-RAY DIFFRACTION99.86
1.77-1.830.24641530.20132587X-RAY DIFFRACTION99.6
1.83-1.90.19271580.18952555X-RAY DIFFRACTION99.27
1.9-1.970.2061320.17052603X-RAY DIFFRACTION99.64
1.97-2.060.20181240.1572641X-RAY DIFFRACTION99.53
2.06-2.170.16921320.16152628X-RAY DIFFRACTION99.89
2.17-2.310.17421290.15762626X-RAY DIFFRACTION99.82
2.31-2.490.19221430.1492632X-RAY DIFFRACTION99.75
2.49-2.740.17561410.15552591X-RAY DIFFRACTION98.41
2.74-3.130.1641450.15322652X-RAY DIFFRACTION99.54
3.13-3.940.16971470.13952632X-RAY DIFFRACTION99.86
3.95-44.170.16841360.15952716X-RAY DIFFRACTION98.45
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)
17.20574981921-0.245902107968-5.375248739221.85478242753-0.07064830224554.628858777650.0215877821179-0.5124612737380.09349034547850.2197967353170.056534701623-0.0764756999297-0.3765067212570.453641008116-0.1228674930310.1439305957190.0299370899528-0.01264586205540.152095206545-0.01809808724210.1226837173537.476010018220.8032440323-2.99434871436
25.38145867391-6.406667882151.854182671327.75943237032-1.956693715011.113466442550.243482357347-0.0563434773182-0.266170241134-0.187286527178-0.1108198855950.3515547092090.195678336124-0.00816664006935-0.1090126927930.1814899259280.02996401721830.00259955659070.166838585968-0.03109686065040.11798214536518.110876871930.6783718255.54526525162
34.54646253334-2.273311696640.186957893362.9487130161-0.2306300647131.56060273071-0.128739823395-0.261438204481-0.300915219654-0.01626075614050.1342560553180.2750320944840.209167881201-0.149628732850.001257209317030.1885416314390.02447000310890.02067808052790.2074265576110.0006212849121070.11530128615615.244810437730.04367119016.96465245602
44.4267977473-5.145660007510.3986758717067.16936557096-1.771246908532.6122276643-0.137760463-0.164856477497-0.1810854993950.1847296875250.1176946302080.259082961016-0.08252168167240.03763941240620.01062536297830.1432237768490.01332864509730.004883942266570.150850021835-0.01664157180790.10447889331819.343557711132.956482716712.3663526207
54.52290483852-1.386773211621.53957206472.77613268754-1.815303783812.870991970810.1327246072890.1320764349030.140261358137-0.170022635469-0.1359585150990.537308241865-0.281087590835-0.409880790277-0.0008759344942910.2142613552640.0893830389408-0.02197075486310.211451709308-0.05148910108220.18134074919710.477590594841.35575084249.77106613034
63.31705227434-0.3739633355810.02599449076171.309448729990.6562958445066.76339178501-0.269023130718-0.495258801806-0.4714135813020.7993357491330.2834542751010.006911914297850.7431011942980.2597548851220.06130609831370.3773143792650.09483738591670.02683401116890.3772613822780.07977080340230.22771015731928.458698290319.131142209214.4683901572
71.455222787480.2687825010990.7552015719726.601245497394.982431139165.788547885930.01920922786250.2549959569540.0710412388542-0.4165734009020.319969589418-0.199518577275-0.6896641850580.74988403673-0.2113378469090.2216497913740.003021232817370.03626012337750.140238300073-0.002173967219710.13833976555119.76077894243.82419116643.23833630645
83.49386634162-2.73928715359-0.01501311910092.79443396874-0.7960626653243.22757893563-0.140487205759-0.0533262588848-0.6664861734210.01893739992420.1897478172910.5094256932840.299516397704-0.357370781292-0.00865767615640.175105216019-0.0291805029220.01223806170820.214064671382-0.006169809828160.2386964310824.761126464916.6158417831-7.2909242773
93.10526886731-2.887873103610.5717428235584.37799530872-0.01875682513241.33894126973-0.1010557484670.00908393271936-0.1723104672410.09064517149090.02301227566770.281808006041-0.0363653279602-0.2128583686670.06323206352480.1685086113580.02785163914940.02677846306740.15367420862-0.01331307470830.11121882655424.829999661323.5269859097-8.46245284715
101.18912747998-1.921655477270.6548162006387.24296866383-0.2707260976831.723113997170.1693619531920.214055462979-0.265134580242-0.273188762051-0.17465599013-0.06898039399750.267619802493-0.0009240547195470.01984486393910.165464814720.02823927898990.03445651911040.135563860872-0.01347616041050.15287392732232.818294200413.0547188051-10.9506947845
111.05345000306-2.346619756890.3663613091595.724733831080.5530663407713.896864332250.3011509772280.7897553957230.339661572526-0.388428174782-0.2903701062410.275983884305-0.299209292013-0.5958711394110.07142727614610.2851638270850.0890801229596-0.0158851828420.3433211011360.0261531492880.15521611999115.91893209235.7035813665-14.0387544165
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'V' and (resid 12 through 26 )VA12 - 261 - 21
22chain 'V' and (resid 27 through 38 )VA27 - 3822 - 33
33chain 'V' and (resid 39 through 65 )VA39 - 6534 - 60
44chain 'V' and (resid 66 through 83 )VA66 - 8361 - 80
55chain 'V' and (resid 84 through 99 )VA84 - 9981 - 99
66chain 'V' and (resid 100 through 107 )VA100 - 107100 - 107
77chain 'W' and (resid 12 through 26 )WB12 - 261 - 23
88chain 'W' and (resid 27 through 45 )WB27 - 4524 - 42
99chain 'W' and (resid 46 through 84 )WB46 - 8443 - 83
1010chain 'W' and (resid 85 through 99 )WB85 - 9984 - 102
1111chain 'W' and (resid 100 through 107 )WB100 - 107103 - 110

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