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- PDB-7ll9: D-Protein RFX-V2 Bound to the VEGFR1 Domain 3 Site on VEGF-A -

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Basic information

Entry
Database: PDB / ID: 7ll9
TitleD-Protein RFX-V2 Bound to the VEGFR1 Domain 3 Site on VEGF-A
Components
  • Isoform L-VEGF189 of Vascular endothelial growth factor A
  • RFX-V2
KeywordsBIOSYNTHETIC PROTEIN / D-protein / Antagonist
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / 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 / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / 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 / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
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
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: 2.9 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 1.0Mar 3, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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-V2
D: RFX-V2
E: Isoform L-VEGF189 of Vascular endothelial growth factor A
F: Isoform L-VEGF189 of Vascular endothelial growth factor A
G: RFX-V2
H: RFX-V2


Theoretical massNumber of molelcules
Total (without water)75,1698
Polymers75,1698
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, VEGF-A is a disulfide linked homodimer based on homology to 3QTK
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.850, 120.437, 120.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23F
14B
24E
15B
25F
16C
26D
17C
27G
18C
28H
19D
29G
110D
210H
111E
211F
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA39 - 1337 - 101
21GLUGLULYSLYSBB39 - 1337 - 101
12GLUGLULYSLYSAA39 - 1347 - 102
22GLUGLULYSLYSEE39 - 1347 - 102
13GLUGLULYSLYSAA39 - 1337 - 101
23GLUGLULYSLYSFF39 - 1337 - 101
14GLUGLULYSLYSBB39 - 1337 - 101
24GLUGLULYSLYSEE39 - 1337 - 101
15HISHISLYSLYSBB37 - 1335 - 101
25HISHISLYSLYSFF37 - 1335 - 101
16DPNDPNDPRDPRCC5 - 575 - 57
26DPNDPNDPRDPRDD5 - 575 - 57
17DPNDPNDPRDPRCC5 - 575 - 57
27DPNDPNDPRDPRGG5 - 575 - 57
18DPNDPNDPRDPRCC5 - 575 - 57
28DPNDPNDPRDPRHH5 - 575 - 57
19DPNDPNDPRDPRDD5 - 575 - 57
29DPNDPNDPRDPRGG5 - 575 - 57
110DPNDPNDPRDPRDD5 - 575 - 57
210DPNDPNDPRDPRHH5 - 575 - 57
111GLUGLULYSLYSEE39 - 1337 - 101
211GLUGLULYSLYSFF39 - 1337 - 101
112DPNDPNDPRDPRGG5 - 575 - 57
212DPNDPNDPRDPRHH5 - 575 - 57

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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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.: 4
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-V2


Mass: 6756.470 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: D-protein composed entirely of D-amino acids / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, Bis-Tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.9→120.44 Å / Num. obs: 22242 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 25.7 / Num. measured all: 285459 / Scaling rejects: 6
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
2.9-3.0812.71.14456735230.7750.321.1472.499.9
8.7-120.4410.60.025977892510.0080.02670.799.1

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QTK

3qtk


Resolution: 2.9→58.52 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.936 / SU B: 74.69 / SU ML: 0.556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.394 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3153 1033 4.7 %RANDOM
Rwork0.2627 ---
obs0.2651 21151 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 247.9 Å2 / Biso mean: 129.323 Å2 / Biso min: 78.17 Å2
Baniso -1Baniso -2Baniso -3
1--7.59 Å2-0 Å20 Å2
2--4.5 Å2-0 Å2
3---3.09 Å2
Refinement stepCycle: final / Resolution: 2.9→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 0 0 4909
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125037
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174512
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6476805
X-RAY DIFFRACTIONr_angle_other_deg1.0671.57410566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8395593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.87922.746193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19115601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1711516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021021
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A25740.13
12B25740.13
21A28420.06
22E28420.06
31A25440.14
32F25440.14
41B25600.13
42E25600.13
51B28160.07
52F28160.07
61C15210.19
62D15210.19
71C17560.09
72G17560.09
81C15060.18
82H15060.18
91D15230.19
92G15230.19
101D15850.18
102H15850.18
111E25360.14
112F25360.14
121G15100.18
122H15100.18
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 87 -
Rwork0.432 1485 -
all-1572 -
obs--100 %
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)
11.6572-2.2442-0.59614.47990.32440.4457-0.0369-1.16630.3285-0.84790.73340.52420.14390.6866-0.69660.98530.0495-0.42751.3068-0.72360.996513.353634.787832.0773
20.8767-0.3767-0.80053.4419-0.47390.9806-0.1848-1.11030.0481-0.58080.34080.6370.18421.0864-0.1560.69680.1266-0.2871.4462-0.04860.209522.625323.984135.0525
32.36090.7723-1.76710.2976-0.89736.1502-0.1727-0.0558-0.2267-0.0693-0.0447-0.1537-0.4903-0.81280.21740.88260.2156-0.080.6370.15320.453115.62515.911212.6382
40.40420.52490.65820.89171.10461.7492-0.11370.56650.04880.17950.55780.0640.37991.0914-0.44411.2447-0.22550.29951.2329-0.42731.057528.261447.501910.6878
51.52570.4997-1.93030.3354-0.10254.76320.0086-0.3314-1.0585-0.0967-0.4797-0.5258-0.705-0.48290.47120.86270.283-0.0430.69970.49261.100230.0615-1.95214.6786
60.71320.8699-0.26241.086-0.51035.2224-0.2211-0.071-1.0401-0.13-0.0374-1.2951-0.7957-0.85540.25850.74910.30440.16240.19160.08191.572539.2544-5.0441-6.275
74.53432.21631.05316.21.22420.3665-0.17850.1425-0.00720.45550.14560.8157-0.04620.10470.0330.88940.08630.20840.3502-0.1670.647432.325917.4355-24.2712
82.6629-1.19771.39673.2403-2.78932.5073-0.0887-0.40721.0312-0.2473-0.624-0.82050.0850.33890.71271.2397-0.4006-0.1550.82130.31190.734844.896419.46217.4103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 134
2X-RAY DIFFRACTION2B37 - 135
3X-RAY DIFFRACTION3C5 - 57
4X-RAY DIFFRACTION4D5 - 57
5X-RAY DIFFRACTION5E39 - 134
6X-RAY DIFFRACTION6F37 - 134
7X-RAY DIFFRACTION7G5 - 57
8X-RAY DIFFRACTION8H5 - 57

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