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- PDB-9s57: The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide -

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Basic information

Entry
Database: PDB / ID: 9s57
TitleThe b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
Components
  • Neuropilin-1
  • Neurosecretory protein VGF
KeywordsSIGNALING PROTEIN / receptor
Function / homology
Function and homology information


endothelial tip cell fate specification / carbohydrate homeostasis / basal dendrite development / otic placode development / basal dendrite arborization / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance ...endothelial tip cell fate specification / carbohydrate homeostasis / basal dendrite development / otic placode development / basal dendrite arborization / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / sensory neuron axon guidance / facial nerve structural organization / trigeminal nerve structural organization / branchiomotor neuron axon guidance / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / protein localization to early endosome / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / motor neuron migration / renal artery morphogenesis / neurofilament / sympathetic neuron projection extension / Neuropilin interactions with VEGF and VEGFR / regulation of vascular endothelial growth factor receptor signaling pathway / angiogenesis involved in coronary vascular morphogenesis / postsynapse organization / vascular endothelial growth factor binding / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / axonogenesis involved in innervation / vascular endothelial growth factor receptor activity / positive regulation of axon extension involved in axon guidance / CHL1 interactions / endothelial cell chemotaxis / retinal ganglion cell axon guidance / regulation of vesicle-mediated transport / semaphorin receptor complex / substrate-dependent cell migration, cell extension / neuropilin signaling pathway / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / coronary artery morphogenesis / motor neuron axon guidance / NGF-stimulated transcription / CRMPs in Sema3A signaling / neural crest cell migration / neuropeptide hormone activity / semaphorin receptor activity / cell migration involved in sprouting angiogenesis / commissural neuron axon guidance / outflow tract septum morphogenesis / artery morphogenesis / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / sprouting angiogenesis / platelet-derived growth factor receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / positive regulation of filopodium assembly / regulation of Cdc42 protein signal transduction / positive regulation of smooth muscle cell migration / positive regulation of cell migration involved in sprouting angiogenesis / growth factor binding / sorting endosome / positive chemotaxis / cytokine binding / vasculogenesis / cellular response to vascular endothelial growth factor stimulus / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / positive regulation of phosphorylation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / response to cAMP / positive regulation of stress fiber assembly / transport vesicle / coreceptor activity / positive regulation of endothelial cell proliferation / animal organ morphogenesis / positive regulation of endothelial cell migration / axon guidance / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / Signal transduction by L1 / GTPase activator activity / growth factor activity / Post-translational protein phosphorylation / response to wounding / neuron migration / regulation of synaptic plasticity / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / mitochondrial membrane / positive regulation of angiogenesis / cell-cell signaling / heparin binding / negative regulation of neuron apoptotic process / angiogenesis
Similarity search - Function
Neurosecretory protein VGF / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...Neurosecretory protein VGF / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Neuropilin-1 / Neurosecretory protein VGF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.569 Å
AuthorsBradshaw, W.J. / Wilkes, A.J.R. / Randall, G.T. / Wang, D. / Katis, V.L. / Gileadi, O. / Gospodinova, K.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 United States
CitationJournal: To Be Published
Title: The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
Authors: Bradshaw, W.J. / Wilkes, A.J.R. / Randall, G.T. / Wang, D. / Katis, V.L. / Gileadi, O. / Gospodinova, K.O.
History
DepositionJul 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: Neurosecretory protein VGF


Theoretical massNumber of molelcules
Total (without water)38,3822
Polymers38,3822
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.541, 34.592, 70.226
Angle α, β, γ (deg.)90.000, 117.208, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neuropilin-1 / Vascular endothelial cell growth factor 165 receptor


Mass: 35883.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Protein/peptide Neurosecretory protein VGF


Mass: 2497.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15240
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
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: 1.84 Å3/Da / Density % sol: 33.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM magnesium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.568→58.278 Å / Num. obs: 26510 / % possible obs: 66.7 % / Redundancy: 19.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.061 / Rrim(I) all: 0.272 / Net I/σ(I): 7.5
Reflection shellResolution: 1.568→1.796 Å / Redundancy: 18.4 % / Rmerge(I) obs: 2.028 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1394 / CC1/2: 0.592 / Rpim(I) all: 0.485 / Rrim(I) all: 2.086 / % possible all: 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.569→58.278 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.148 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2388 1509 5.692 %
Rwork0.1708 25000 -
all0.175 --
obs-26509 66.807 %
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: 20.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å2-0 Å2-0.013 Å2
2---0.123 Å2-0 Å2
3---0.085 Å2
Refinement stepCycle: LAST / Resolution: 1.569→58.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 307 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122678
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162532
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.8233627
X-RAY DIFFRACTIONr_angle_other_deg0.531.7765855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9565337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.582521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1110489
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.6510121
X-RAY DIFFRACTIONr_chiral_restr0.0790.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
X-RAY DIFFRACTIONr_nbd_refined0.1990.2452
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22400
X-RAY DIFFRACTIONr_nbtor_refined0.180.21278
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.223
X-RAY DIFFRACTIONr_nbd_other0.2250.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1320.21
X-RAY DIFFRACTIONr_mcbond_it1.9461.9871303
X-RAY DIFFRACTIONr_mcbond_other1.9461.9871303
X-RAY DIFFRACTIONr_mcangle_it3.0493.5651631
X-RAY DIFFRACTIONr_mcangle_other3.0483.5651632
X-RAY DIFFRACTIONr_scbond_it3.0882.3321375
X-RAY DIFFRACTIONr_scbond_other3.0862.3321376
X-RAY DIFFRACTIONr_scangle_it4.7844.1021988
X-RAY DIFFRACTIONr_scangle_other4.7824.1021989
X-RAY DIFFRACTIONr_lrange_it6.8124.3693078
X-RAY DIFFRACTIONr_lrange_other6.72422.7542995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.569-1.6100.2759X-RAY DIFFRACTION0.3128
1.61-1.6540.20840.28180X-RAY DIFFRACTION2.9619
1.654-1.7020.35530.309119X-RAY DIFFRACTION4.4364
1.702-1.7540.334240.265344X-RAY DIFFRACTION13.7365
1.754-1.8110.359610.2661021X-RAY DIFFRACTION41.4559
1.811-1.8750.2681150.2481640X-RAY DIFFRACTION69.8925
1.875-1.9460.3081310.2412027X-RAY DIFFRACTION88.8797
1.946-2.0250.2541260.2132191X-RAY DIFFRACTION98.3029
2.025-2.1150.2411470.2032087X-RAY DIFFRACTION99.7321
2.115-2.2180.282940.1862041X-RAY DIFFRACTION99.8597
2.218-2.3380.254900.1711961X-RAY DIFFRACTION99.9026
2.338-2.4790.203970.1741847X-RAY DIFFRACTION99.9486
2.479-2.650.2421010.1681738X-RAY DIFFRACTION99.8371
2.65-2.8620.2351100.1671586X-RAY DIFFRACTION100
2.862-3.1340.214920.1611491X-RAY DIFFRACTION99.9369
3.134-3.5030.2391120.1431310X-RAY DIFFRACTION100
3.503-4.0420.199570.131204X-RAY DIFFRACTION100
4.042-4.9450.177530.1251049X-RAY DIFFRACTION99.9093
4.945-6.9680.237760.15772X-RAY DIFFRACTION100
6.968-58.2780.338160.198483X-RAY DIFFRACTION100

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