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- PDB-5j1x: X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. -

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Basic information

Entry
Database: PDB / ID: 5j1x
TitleX-ray structure of neuropilin-1 b1 domain complexed with Arg-5 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~2~-(tert-butoxycarbonyl)-L-arginine / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Feb 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 1.3Jul 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 1.4Jan 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 / 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
C: Neuropilin-1
D: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8459
Polymers71,6694
Non-polymers1,1755
Water7,764431
1
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1922
Polymers17,9171
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1922
Polymers17,9171
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1922
Polymers17,9171
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2703
Polymers17,9171
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.590, 90.480, 81.890
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILEAA274 - 4265 - 157
21LYSLYSILEILEBB274 - 4265 - 157
12PHEPHEILEILEAA273 - 4264 - 157
22PHEPHEILEILECC273 - 4264 - 157
13PHEPHETHRTHRAA273 - 4274 - 158
23PHEPHETHRTHRDD273 - 4274 - 158
14LYSLYSILEILEBB274 - 4265 - 157
24LYSLYSILEILECC274 - 4265 - 157
15LYSLYSILEILEBB274 - 4265 - 157
25LYSLYSILEILEDD274 - 4265 - 157
16PHEPHEILEILECC273 - 4264 - 157
26PHEPHEILEILEDD273 - 4264 - 157

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 4
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-AR5 / N~2~-(tert-butoxycarbonyl)-L-arginine


Mass: 274.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H22N4O4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: needles
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 18% w/v 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: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→41 Å / Num. obs: 47057 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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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: 2.1→80.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.395 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1728 5 %RANDOM
Rwork0.18157 ---
obs0.18369 33165 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.59 Å2
2---0.1 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→80.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4953 0 80 431 5464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.025198
X-RAY DIFFRACTIONr_bond_other_d0.0070.024897
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9467061
X-RAY DIFFRACTIONr_angle_other_deg1.2182.97711303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7824.089225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53515897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1361529
X-RAY DIFFRACTIONr_chiral_restr0.090.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215826
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021187
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_it0.9911.6722496
X-RAY DIFFRACTIONr_mcbond_other0.9881.6692491
X-RAY DIFFRACTIONr_mcangle_it1.7162.4983112
X-RAY DIFFRACTIONr_mcangle_other1.7152.4983113
X-RAY DIFFRACTIONr_scbond_it1.291.8812702
X-RAY DIFFRACTIONr_scbond_other1.291.8822703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1822.7523942
X-RAY DIFFRACTIONr_long_range_B_refined4.28314.0945982
X-RAY DIFFRACTIONr_long_range_B_other4.28314.0995983
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A183860.08
12B183860.08
21A183460.1
22C183460.1
31A184420.11
32D184420.11
41B185700.09
42C185700.09
51B184940.1
52D184940.1
61C191020.07
62D191020.07
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 142 -
Rwork0.234 2426 -
obs--99.77 %
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)
10.77360.16640.31150.30210.43960.784-0.02070.03110.05450.0085-0.00750.0215-0.0227-0.00570.02820.0126-0.0003-0.01070.00650.00470.055840.110319.246621.2856
20.60020.10380.34890.6270.56840.9376-0.03690.0649-0.00710.0058-0.06210.0208-0.114-0.07710.0990.03680.0135-0.02650.0295-0.0150.026534.130619.13960.8675
31.3286-0.6605-0.25840.85650.23040.80390.08910.09610.00540.0003-0.04540.00430.0129-0.0277-0.04370.01380.0015-0.00320.02820.00010.006851.3619-3.60642.4283
40.62-0.3391-0.16260.93640.21270.68750.05210.0896-0.00230.0430.0072-0.0449-0.0106-0.0588-0.05940.01170.0109-0.00530.0350.00090.02157.6529-3.61712.2189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A273 - 427
2X-RAY DIFFRACTION2B274 - 427
3X-RAY DIFFRACTION3C272 - 427
4X-RAY DIFFRACTION4D273 - 427

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