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- PDB-9eou: Crystal Structure of the b1b2 domains from Human Neuropilin-1 in ... -

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Basic information

Entry
Database: PDB / ID: 9eou
TitleCrystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.
Components
  • Neuropilin-1
  • Osteopontin
KeywordsSTRUCTURAL PROTEIN / angiogenesis / Neuropilin-1
Function / homology
Function and homology information


negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / biomineral tissue development / dichotomous subdivision of terminal units involved in salivary gland branching ...negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / biomineral tissue development / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / neurofilament / response to macrophage colony-stimulating factor / postsynapse organization / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / motor neuron migration / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / CHL1 interactions / vascular endothelial growth factor receptor activity / regulation of vesicle-mediated transport / Signaling by ROBO receptors / angiogenesis involved in coronary vascular morphogenesis / neuropilin signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Signaling by PDGF / coronary artery morphogenesis / hepatocyte growth factor receptor signaling pathway / substrate-dependent cell migration, cell extension / outflow tract septum morphogenesis / semaphorin receptor activity / cellular response to testosterone stimulus / ion binding / CRMPs in Sema3A signaling / response to vitamin D / commissural neuron axon guidance / RUNX3 Regulates Immune Response and Cell Migration / semaphorin receptor complex / extracellular matrix binding / cell migration involved in sprouting angiogenesis / axonal fasciculation / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / response to steroid hormone / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / positive chemotaxis / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / decidualization / cellular response to vascular endothelial growth factor stimulus / positive regulation of bone resorption / small molecule binding / vasculogenesis / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / embryo implantation / Degradation of the extracellular matrix / positive regulation of endothelial cell migration / GTPase activator activity / Signal transduction by L1 / cytokine activity / cell projection
Similarity search - Function
Osteopontin / Osteopontin, conserved site / Osteopontin / Osteopontin signature. / Osteopontin / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) ...Osteopontin / Osteopontin, conserved site / Osteopontin / Osteopontin signature. / Osteopontin / 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 / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / Osteopontin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCaing-Carlsson, R. / Duelli, A. / Walse, B.
Funding support Denmark, Sweden, 3items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
Swedish Research Council Sweden
Vinnova Sweden
CitationJournal: Pharmacol Res / Year: 2024
Title: Identification of an osteopontin-derived peptide that binds neuropilin-1 and activates vascular repair responses and angiogenesis.
Authors: Chen, Y. / Gialeli, C. / Shen, J. / Duner, P. / Walse, B. / Duelli, A. / Caing-Carlsson, R. / Blom, A.M. / Zibert, J.R. / Nilsson, A.H. / Alenfall, J. / Liang, C. / Nilsson, J.
History
DepositionMar 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 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: Neuropilin-1
P: Osteopontin


Theoretical massNumber of molelcules
Total (without water)37,7352
Polymers37,7352
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint0 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.690, 34.910, 69.970
Angle α, β, γ (deg.)90.00, 102.20, 90.00
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: 36119.980 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 K-12 (bacteria) / References: UniProt: O14786
#2: Protein/peptide Osteopontin / Bone sialoprotein 1 / Nephropontin / Secreted phosphoprotein 1 / SPP-1 / Urinary stone protein / Uropontin


Mass: 1614.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10451
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate pH 6.0, 9% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→42.57 Å / Num. obs: 45579 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 1
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 2252 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.57 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.946 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20249 2255 4.9 %RANDOM
Rwork0.16933 ---
obs0.171 43313 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20.3 Å2
2---1.18 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.55→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 0 231 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132620
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182493
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.6493545
X-RAY DIFFRACTIONr_angle_other_deg1.4531.5855754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35121.329143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19515480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4171522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022951
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02633
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_it1.792.2451267
X-RAY DIFFRACTIONr_mcbond_other1.7892.2451266
X-RAY DIFFRACTIONr_mcangle_it2.6473.3551582
X-RAY DIFFRACTIONr_mcangle_other2.6463.3551583
X-RAY DIFFRACTIONr_scbond_it2.8172.6121353
X-RAY DIFFRACTIONr_scbond_other2.8172.6121353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3563.7671956
X-RAY DIFFRACTIONr_long_range_B_refined5.89626.3422882
X-RAY DIFFRACTIONr_long_range_B_other5.89526.3392883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 192 -
Rwork0.297 3186 -
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)
10.11980.13630.30750.31580.20790.9229-0.0033-0.01760.03570.0093-0.04190.0967-0.0087-0.0170.04510.01260.01060.00780.0341-0.01440.0348.9066-5.942834.5056
20000000000000000.0203000.020300.0203000

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