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- PDB-5ijr: X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand. -

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Basic information

Entry
Database: PDB / ID: 5ijr
TitleX-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
ComponentsNeuropilin-1
KeywordsSIGNALING PROTEIN / Neuropilin-1 / Angiogenesis
Function / homology
Function and homology information


endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration ...endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / 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 / trigeminal nerve structural organization / sensory neuron axon guidance / postsynapse organization / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / negative regulation of axon extension involved in axon guidance / axon extension involved in axon guidance / renal artery morphogenesis / VEGF-activated neuropilin signaling pathway / neurofilament / sympathetic neuron projection extension / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / endothelial cell chemotaxis / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / axonogenesis involved in innervation / CHL1 interactions / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / CRMPs in Sema3A signaling / semaphorin receptor activity / commissural neuron axon guidance / outflow tract septum morphogenesis / motor neuron axon guidance / regulation of Cdc42 protein signal transduction / axonal fasciculation / cell migration involved in sprouting angiogenesis / neural crest cell migration / sprouting angiogenesis / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of smooth muscle cell migration / positive chemotaxis / growth factor binding / cytokine binding / sorting endosome / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / vasculogenesis / positive regulation of phosphorylation / coreceptor activity / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / GTPase activator activity / axon guidance / animal organ morphogenesis / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / mitochondrial membrane / vascular endothelial growth factor receptor activity / response to wounding / neuron migration / positive regulation of angiogenesis / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / negative regulation of neuron apoptotic process / postsynaptic membrane / Attachment and Entry / early endosome / receptor complex / positive regulation of ERK1 and ERK2 cascade / neuron projection
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / 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 domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
L-HOMOARGININE / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsFotinou, C. / Rana, R. / Djordjevic, S. / Yelland, T.
CitationJournal: FEBS J. / Year: 2018
Title: Architecture and hydration of the arginine-binding site of neuropilin-1.
Authors: Mota, F. / Fotinou, C. / Rana, R.R. / Chan, A.W.E. / Yelland, T. / Arooz, M.T. / O'Leary, A.P. / Hutton, J. / Frankel, P. / Zachary, I. / Selwood, D. / Djordjevic, S.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: 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
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7114
Polymers35,4442
Non-polymers2662
Water5,044280
1
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9102
Polymers17,7221
Non-polymers1881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8002
Polymers17,7221
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.139, 88.936, 40.962
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 274 - 426 / Label seq-ID: 3 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 17722.092 Da / Num. of mol.: 2 / Fragment: b1 domain, UNP residues 273-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Plasmid: pET15b-TEV-nrp1b1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta-gami2(DE3)pLysS / References: UniProt: O14786
#2: Chemical ChemComp-HRG / L-HOMOARGININE


Type: L-peptide linking / Mass: 188.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N4O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 28% w/v PEG3350, 0.2 M AmCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.52→40.68 Å / Num. obs: 41807 / % possible obs: 95.4 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→40.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.862 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21298 2093 5 %RANDOM
Rwork0.1811 ---
obs0.18264 39714 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-1.08 Å2
2---1.57 Å2-0 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.52→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 17 280 2772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022565
X-RAY DIFFRACTIONr_bond_other_d0.0090.022408
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9473481
X-RAY DIFFRACTIONr_angle_other_deg1.5432.9925561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3915314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80124.196112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6951514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212875
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02583
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_it0.9831.1411245
X-RAY DIFFRACTIONr_mcbond_other0.9831.1411245
X-RAY DIFFRACTIONr_mcangle_it1.6511.7041554
X-RAY DIFFRACTIONr_mcangle_other1.6511.7051555
X-RAY DIFFRACTIONr_scbond_it1.6261.3761320
X-RAY DIFFRACTIONr_scbond_other1.6251.381321
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5411.9791925
X-RAY DIFFRACTIONr_long_range_B_refined5.17210.5922988
X-RAY DIFFRACTIONr_long_range_B_other5.17110.6112989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18270 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 126 -
Rwork0.301 2114 -
obs--69.41 %
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)
10.3668-0.49440.21560.7454-0.24030.3810.0362-0.0069-0.0205-0.0916-0.0270.00180.0088-0.0131-0.00920.0617-0.00950.02190.04780.00460.013936.19-21.497242.6309
20.20360.046-0.09821.61770.17360.0739-0.0939-0.11120.0475-0.21890.07190.42940.01640.07220.0220.06660.0302-0.0710.0819-0.00340.121255.79311.198556.8921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A274 - 427
2X-RAY DIFFRACTION2B272 - 427

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