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- PDB-9ju1: Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A -

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Basic information

Entry
Database: PDB / ID: 9ju1
TitleHelix-loop-helix peptide (VS42-LR3) in complex with VEGF-A
Components
  • VS42-LR3
  • Vascular endothelial growth factor A, long form
KeywordsIMMUNE SYSTEM/DE NOVO PROTEIN / Helix-loop-helix / Inhibitor / complex / DE NOVO PROTEIN / IMMUNE SYSTEM-DE NOVO PROTEIN complex
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 / negative regulation of adherens junction organization / 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 / 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 / endothelial cell chemotaxis / lung vasculature development / vascular wound healing / positive regulation of protein localization to early endosome / eye photoreceptor cell development / regulation of hematopoietic progenitor cell differentiation / camera-type eye morphogenesis / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of protein autophosphorylation / positive regulation of branching involved in ureteric bud morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / transmembrane receptor protein tyrosine kinase activator activity / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / 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 leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / 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 / artery morphogenesis / positive regulation of DNA biosynthetic process / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of epithelial to mesenchymal transition / 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 / monocyte differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / macrophage differentiation / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / positive regulation of focal adhesion assembly / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / heart morphogenesis / vasculogenesis / cell maturation / ovarian follicle development / lactation / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / extracellular matrix / homeostasis of number of cells within a tissue
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
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKamo, M. / Michigami, M. / Inaka, K. / Furubayashi, N. / Kaito, S. / Kobayashi, Y. / Shinohara, Y. / Fujii, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP24am121036 Japan
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Structural insights into molecular-targeting helix-loop-helix peptide against vascular endothelial growth factor-A.
Authors: Michigami, M. / Notsu, K. / Kamo, M. / Hirokawa, T. / Kinoshita, T. / Inaka, K. / Nakase, I. / Fujii, I.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: VS42-LR3
A: Vascular endothelial growth factor A, long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7843
Polymers16,6882
Non-polymers961
Water2,864159
1
C: VS42-LR3
A: Vascular endothelial growth factor A, long form
hetero molecules

C: VS42-LR3
A: Vascular endothelial growth factor A, long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5686
Polymers33,3764
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6240 Å2
ΔGint-58 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.982, 42.982, 309.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-236-

HOH

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Components

#1: Protein/peptide VS42-LR3


Mass: 4739.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Vascular endothelial growth factor A, long form / L-VEGF / Vascular permeability factor / VPF


Mass: 11948.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3) / References: UniProt: P15692
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 0.2M NaCl, 2.5M Ammonium Sulfate, 0.04% NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→44.24 Å / Num. obs: 31964 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Χ2: 0.7 / Net I/σ(I): 22.3 / Num. measured all: 652847
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.786 / Num. measured all: 30171 / Num. unique obs: 1558 / CC1/2: 0.92 / Rpim(I) all: 0.183 / Rrim(I) all: 0.807 / Χ2: 0.15 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→37.251 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.212 / SU B: 1.603 / SU ML: 0.061 / Average fsc free: 0.9437 / Average fsc work: 0.9583 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1533 4.822 %RANDOM
Rwork0.2156 30258 --
all0.217 ---
obs-31791 99.981 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.497 Å20.248 Å20 Å2
2--0.497 Å20 Å2
3----1.611 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 5 159 1281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161061
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.8511554
X-RAY DIFFRACTIONr_angle_other_deg0.6271.7662465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.01354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51710207
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.0711056
X-RAY DIFFRACTIONr_chiral_restr0.0910.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined0.2070.2201
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2925
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.222
X-RAY DIFFRACTIONr_nbd_other0.1550.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.233
X-RAY DIFFRACTIONr_mcbond_it2.8542.746559
X-RAY DIFFRACTIONr_mcbond_other2.8462.745559
X-RAY DIFFRACTIONr_mcangle_it4.1744.915696
X-RAY DIFFRACTIONr_mcangle_other4.1754.918697
X-RAY DIFFRACTIONr_scbond_it4.6373.367591
X-RAY DIFFRACTIONr_scbond_other4.6333.37592
X-RAY DIFFRACTIONr_scangle_it7.1975.856858
X-RAY DIFFRACTIONr_scangle_other7.1935.859859
X-RAY DIFFRACTIONr_lrange_it8.90735.941285
X-RAY DIFFRACTIONr_lrange_other8.86634.1751262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.3391150.29521880.29723030.9170.9291000.279
1.488-1.5280.3121050.26720920.26921970.920.9421000.242
1.528-1.5730.2791090.2620310.26121400.9390.9461000.236
1.573-1.6210.26910.25820270.25821180.9510.951000.229
1.621-1.6740.28980.25119460.25220440.9410.9541000.222
1.674-1.7330.316990.24718900.2519890.9260.9571000.216
1.733-1.7980.319890.2518330.25319220.9270.9561000.22
1.798-1.8710.302980.23217650.23618630.9420.9611000.206
1.871-1.9540.277980.2416970.24217950.9440.9581000.218
1.954-2.0490.294660.24516240.24716900.9340.961000.227
2.049-2.160.279910.22315470.22616380.9470.9691000.209
2.16-2.290.24710.2114640.21115350.9560.9711000.2
2.29-2.4480.234700.20214030.20414730.970.9721000.195
2.448-2.6430.255650.2113270.21213920.9550.971000.204
2.643-2.8930.254630.20812310.2112940.9550.971000.205
2.893-3.2330.21640.22111190.2211830.9690.9681000.224
3.233-3.7280.238530.19310080.19510610.9590.9771000.205
3.728-4.5540.19480.1648640.1669120.9770.9841000.18
4.554-6.3930.165230.2067300.2057530.9820.981000.229
6.393-37.2510.291170.2534720.2554940.9610.95198.98790.278

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