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- PDB-7p5u: Neuropilin-b1 in a complex with a VEGFB-derived peptide -

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Basic information

Entry
Database: PDB / ID: 7p5u
TitleNeuropilin-b1 in a complex with a VEGFB-derived peptide
Components
  • MGC0122
  • Neuropilin-1Neuropilin 1
KeywordsSIGNALING PROTEIN / Neuropilin / VEGFB / Complex / peptide-lipidation
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-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFotinou, C. / Rhana, R. / Yelland, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/10/52/28448 United Kingdom
CitationJournal: To Be Published
Title: Neuropilin-b1 in a complex with a VEGFB-derived peptide
Authors: Fotinou, C. / Rhana, R. / Yelland, T.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
AAA: Neuropilin-1
BBB: Neuropilin-1
CCC: MGC0122
EEE: MGC0122


Theoretical massNumber of molelcules
Total (without water)38,9224
Polymers38,9224
Non-polymers00
Water3,369187
1
AAA: Neuropilin-1
CCC: MGC0122


  • defined by author&software
  • Evidence: surface plasmon resonance
  • 19.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)19,4612
Polymers19,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint0 kcal/mol
Surface area7790 Å2
MethodPISA
2
BBB: Neuropilin-1
EEE: MGC0122


  • defined by author&software
  • Evidence: surface plasmon resonance
  • 19.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)19,4612
Polymers19,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint0 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.496, 74.350, 91.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 275 - 426 / Label seq-ID: 6 - 157

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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
Details: First five residues of this chain are not visible in the electron density maps
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Protein/peptide MGC0122


Mass: 1543.711 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Only the last three C-terminal residues of the peptide are visible in the electron density maps. Other residues are disordered.
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 10 to 30% PEG 3350 + 0.2 M ammonium chloride

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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 PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→57.684 Å / Num. obs: 50849 / % possible obs: 96.7 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.67 Å / Num. unique obs: 4924 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEX

1kex


Resolution: 1.6→57.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.292 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2139 2189 4.963 %
Rwork0.1882 41919 -
all0.189 --
obs-44108 99.36 %
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: 19.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.034 Å20 Å2-0 Å2
2---0.029 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.6→57.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 0 187 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132657
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182489
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.6573617
X-RAY DIFFRACTIONr_angle_other_deg1.511.5835758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9035331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35622.19137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11815465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.081517
X-RAY DIFFRACTIONr_chiral_restr0.10.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
X-RAY DIFFRACTIONr_nbd_refined0.1830.2402
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22331
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21258
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2145
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.219
X-RAY DIFFRACTIONr_nbd_other0.2770.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1740.21
X-RAY DIFFRACTIONr_mcbond_it1.8621.5931282
X-RAY DIFFRACTIONr_mcbond_other1.8611.5931281
X-RAY DIFFRACTIONr_mcangle_it2.7992.3811600
X-RAY DIFFRACTIONr_mcangle_other2.7992.3821601
X-RAY DIFFRACTIONr_scbond_it2.7781.9251375
X-RAY DIFFRACTIONr_scbond_other2.7781.9241375
X-RAY DIFFRACTIONr_scangle_it4.2192.7612008
X-RAY DIFFRACTIONr_scangle_other4.2192.7612008
X-RAY DIFFRACTIONr_lrange_it5.5818.6172914
X-RAY DIFFRACTIONr_lrange_other5.57918.6152915
X-RAY DIFFRACTIONr_ncsr_local_group_10.1190.054945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.119170.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.119170.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.2861690.29129610.2932250.8540.84597.05430.263
1.642-1.6860.3071660.27529520.27631580.8490.86698.73340.244
1.686-1.7350.2681530.23829050.23930930.8850.89798.86840.206
1.735-1.7890.2371530.21427840.21529630.9210.92599.12250.183
1.789-1.8470.2561510.20127280.20429010.9020.92899.24160.172
1.847-1.9120.2091300.18626410.18727900.9360.94299.3190.157
1.912-1.9840.2311270.18725590.18926950.9340.94599.6660.16
1.984-2.0650.2191350.17724790.17926250.940.95199.58090.157
2.065-2.1570.21200.17923830.1825140.9550.95499.56240.156
2.157-2.2620.2291120.17322740.17623950.9380.95499.62420.152
2.262-2.3840.204990.17121840.17322860.9520.95799.86880.152
2.384-2.5280.1921120.17320730.17421870.9530.95299.90850.152
2.528-2.7030.221090.17219350.17420450.9440.95699.95110.153
2.703-2.9190.184750.17918170.1818930.9430.9599.94720.163
2.919-3.1960.206730.19317070.19317800.9510.9511000.177
3.196-3.5720.22930.19215230.19416160.9480.9551000.181
3.572-4.1220.181750.16913620.1714370.9660.9671000.164
4.122-5.0420.186670.15811520.15912190.970.9771000.155
5.042-7.1040.206430.1929380.1939810.9670.9661000.182
7.104-57.6840.225270.245620.2395890.9530.9441000.226
Refinement TLS params.Method: refined / Origin x: 62.061 Å / Origin y: 12.294 Å / Origin z: 26.195 Å
111213212223313233
T0.0297 Å2-0.0008 Å2-0.0095 Å2-0.0253 Å2-0.0034 Å2--0.0226 Å2
L1.0804 °20.341 °20.4175 °2-0.6283 °20.2384 °2--0.9499 °2
S-0.0542 Å °-0.0663 Å °-0.0814 Å °0.0443 Å °0.0333 Å °-0.0598 Å °-0.1314 Å °0.0509 Å °0.0209 Å °
Refinement TLS groupSelection: ALL

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