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- PDB-5jhk: X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand. -

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Basic information

Entry
Database: PDB / ID: 5jhk
TitleX-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand.
ComponentsNeuropilin-1Neuropilin 1
KeywordsSIGNALING PROTEIN / Neuropilin-1 / Angiogenesis
Function / homology
Function and homology information


positive regulation of cytokine activity / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / 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 ...positive regulation of cytokine activity / endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / neurofilament / basal dendrite arborization / 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 / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / postsynapse organization / 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 / motor neuron migration / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / vascular endothelial growth factor binding / sympathetic ganglion development / axonogenesis involved in innervation / 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 / substrate-dependent cell migration, cell extension / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / angiogenesis involved in coronary vascular morphogenesis / hepatocyte growth factor receptor signaling pathway / neuropilin signaling pathway / coronary artery morphogenesis / outflow tract septum morphogenesis / regulation of Cdc42 protein signal transduction / semaphorin receptor activity / commissural neuron axon guidance / CRMPs in Sema3A signaling / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / axonal fasciculation / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / branching involved in blood vessel morphogenesis / cellular response to hepatocyte growth factor stimulus / positive regulation of cell migration involved in sprouting angiogenesis / 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 / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / 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 / GTPase activator activity / positive regulation of endothelial cell migration / Signal transduction by L1 / integrin-mediated signaling pathway / axon guidance / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / receptor complex / early endosome
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) / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain ...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 / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / 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
N-(benzenecarbonyl)glycyl-L-arginine / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionApr 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 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 1.2Apr 25, 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 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,1703
Polymers35,8352
Non-polymers3351
Water3,711206
1
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2532
Polymers17,9171
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-1


Theoretical massNumber of molelcules
Total (without water)17,9171
Polymers17,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.376, 90.781, 40.965
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17917.291 Da / Num. of mol.: 2
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(DE3) (bacteria) / Variant (production host): Rosetta-gami2-pLysS / References: UniProt: O14786
#2: Chemical ChemComp-6K8 / N-(benzenecarbonyl)glycyl-L-arginine


Mass: 335.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N5O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 30%PEG3350+0,2M NH4Cl

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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 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.63→40.54 Å / Num. obs: 36381 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.9
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 1.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kex

1kex


Resolution: 1.8→45.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.915 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21509 1303 4.8 %RANDOM
Rwork0.16728 ---
obs0.16957 25765 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.78 Å2
2---0.16 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 24 206 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022580
X-RAY DIFFRACTIONr_bond_other_d0.0010.022414
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9413499
X-RAY DIFFRACTIONr_angle_other_deg0.8842.9885573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2624.107112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26215444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8011514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
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_it1.3281.6261249
X-RAY DIFFRACTIONr_mcbond_other1.3291.6251247
X-RAY DIFFRACTIONr_mcangle_it2.0912.4271557
X-RAY DIFFRACTIONr_mcangle_other2.092.4271558
X-RAY DIFFRACTIONr_scbond_it1.8191.9071331
X-RAY DIFFRACTIONr_scbond_other1.8181.9091332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9632.761942
X-RAY DIFFRACTIONr_long_range_B_refined5.23614.2432959
X-RAY DIFFRACTIONr_long_range_B_other5.08313.932901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 118 -
Rwork0.269 1898 -
obs--99.8 %
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)
10.6099-0.86120.16391.2641-0.32220.34570.10090.0173-0.0211-0.1735-0.04970.02160.0659-0.029-0.05120.0614-0.01030.00520.05630.00330.054734.8066-21.68542.8396
20.79240.0997-0.23571.00620.48520.5408-0.08660.00180.0437-0.08170.02870.1467-0.00540.00920.05790.01620.0003-0.02520.0512-0.00930.088354.60020.934256.9944
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A274 - 427
2X-RAY DIFFRACTION2B270 - 427

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