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- PDB-9kku: Helix-loop-helix peptide (M49) in complex with VEGF-A -

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Basic information

Entry
Database: PDB / ID: 9kku
TitleHelix-loop-helix peptide (M49) in complex with VEGF-A
Components
  • M49
  • 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 / 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
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 Helix-Loop-Helix Peptides for "Ligand-Targeting" Intracellular Drug Delivery via VEGF Receptor-Mediated Endocytosis.
Authors: Michigami, M. / Kira, R. / Kamo, M. / Hirokawa, T. / Kinoshita, T. / Inaka, K. / Nakase, I. / Fujii, I.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vascular endothelial growth factor A, long form
B: Vascular endothelial growth factor A, long form
C: M49
D: M49


Theoretical massNumber of molelcules
Total (without water)33,2854
Polymers33,2854
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-59 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.260, 66.420, 76.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vascular endothelial growth factor A, long form / L-VEGF / Vascular permeability factor / VPF


Mass: 11948.680 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) / Strain (production host): Origami2 (DE3) / References: UniProt: P15692
#2: Protein/peptide M49


Mass: 4693.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5.6
Details: 0.2M NH4-AcOH pH 5.6, 14% PEG 3350, 20% 2-Propanol, 0.2M CaCl2,, 0.4M NaCl, 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: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.45→44.24 Å / Num. obs: 47938 / % 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
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
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→44.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.797 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25038 2518 5 %RANDOM
Rwork0.21691 ---
obs0.21854 47938 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.784 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0 Å20 Å2
2--2.52 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.46→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 161 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132256
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172099
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.6523049
X-RAY DIFFRACTIONr_angle_other_deg1.391.5744922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97124.019107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.745158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.472.3671100
X-RAY DIFFRACTIONr_mcbond_other2.4672.3651099
X-RAY DIFFRACTIONr_mcangle_it3.6833.5291368
X-RAY DIFFRACTIONr_mcangle_other3.6843.5331369
X-RAY DIFFRACTIONr_scbond_it3.312.7411156
X-RAY DIFFRACTIONr_scbond_other3.2762.7381155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0533.9581681
X-RAY DIFFRACTIONr_long_range_B_refined7.13229.8972504
X-RAY DIFFRACTIONr_long_range_B_other7.08629.7332472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.497 Å
RfactorNum. reflection% reflection
Rfree0.282 200 -
Rwork0.281 3477 -
obs--99.73 %

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