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- PDB-7ll8: D-Protein RFX-V1 Bound to the VEGFR1 Domain 2 Site on VEGF-A -

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Basic information

Entry
Database: PDB / ID: 7ll8
TitleD-Protein RFX-V1 Bound to the VEGFR1 Domain 2 Site on VEGF-A
Components
  • Isoform L-VEGF189 of Vascular endothelial growth factor A
  • RFX-V1
KeywordsBIOSYNTHETIC PROTEIN / D-protein / Antagonist
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 / endothelial cell chemotaxis / camera-type eye morphogenesis / 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 branching involved in ureteric bud morphogenesis / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of leukocyte migration / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / cell migration involved in sprouting angiogenesis / artery morphogenesis / branching involved in blood vessel morphogenesis / cardiac muscle cell development / 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 / positive regulation of neuroblast proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / positive regulation of cell division / positive regulation of sprouting angiogenesis / positive chemotaxis / mesoderm development / ovarian follicle development / chemoattractant activity / cell maturation / outflow tract morphogenesis / monocyte differentiation / lung development / vasculogenesis / macrophage differentiation / fibronectin binding / 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 / negative regulation of miRNA transcription / positive regulation of cell adhesion / 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
polypeptide(D) / polypeptide(D) (> 10) / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMarinec, P.S. / Landgraf, K.E. / Uppalapati, M. / Chen, G. / Xie, D. / Jiang, Q. / Zhao, Y. / Petriello, A. / Deshayes, K. / Kent, S.B.H. ...Marinec, P.S. / Landgraf, K.E. / Uppalapati, M. / Chen, G. / Xie, D. / Jiang, Q. / Zhao, Y. / Petriello, A. / Deshayes, K. / Kent, S.B.H. / Ault-Riche, D. / Sidhu, S.S.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: A Non-immunogenic Bivalent d-Protein Potently Inhibits Retinal Vascularization and Tumor Growth.
Authors: Marinec, P.S. / Landgraf, K.E. / Uppalapati, M. / Chen, G. / Xie, D. / Jiang, Q. / Zhao, Y. / Petriello, A. / Deshayes, K. / Kent, S.B.H. / Ault-Riche, D. / Sidhu, S.S.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 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

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Assembly

Deposited unit
A: Isoform L-VEGF189 of Vascular endothelial growth factor A
B: Isoform L-VEGF189 of Vascular endothelial growth factor A
C: RFX-V1
D: RFX-V1


Theoretical massNumber of molelcules
Total (without water)35,7394
Polymers35,7394
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, VEGF-A is a disulfide linked homodimer based on homology to 3QTK
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-59 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.867, 69.080, 89.422
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 Isoform L-VEGF189 of Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 12035.758 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 (E. coli) / References: UniProt: P15692
#2: Protein RFX-V1


Mass: 5833.699 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D-protein composed entirely of D-amino acids / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / Details: calcium chloride, Tris, PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.31→46.13 Å / Num. obs: 17391 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Net I/σ(I): 25.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.396.50.2671091216800.9760.1130.297100
8.95-46.095.20.02418423550.9990.0120.02751.899.2

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QTK

3qtk


Resolution: 2.31→46.13 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.83 / SU B: 8.665 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3142 915 5.3 %RANDOM
Rwork0.2603 ---
obs0.263 16353 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.66 Å2 / Biso mean: 40.108 Å2 / Biso min: 21.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.31→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 0 118 2468
Biso mean---40.88 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122438
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172224
X-RAY DIFFRACTIONr_angle_refined_deg1.241.6423307
X-RAY DIFFRACTIONr_angle_other_deg0.9471.5715193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16723.25686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.861158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
LS refinement shellResolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 78 -
Rwork0.288 1178 -
all-1256 -
obs--99.92 %

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