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- PDB-8c5g: Structure of human Neuropilin-1 b1b2 domains in complex with Chlo... -

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Basic information

Entry
Database: PDB / ID: 8c5g
TitleStructure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus)
Components
  • Chlorotoxin
  • Neuropilin-1
KeywordsTOXIN / Cancer / Co-receptor / protein-protein complex / Teranostic
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 / peptidase inhibitor activity / 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 / chloride channel regulator activity / 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 / toxin activity / cytoplasmic vesicle / angiogenesis / negative regulation of neuron apoptotic process / postsynaptic membrane / Attachment and Entry / early endosome
Similarity search - Function
Scorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily 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. ...Scorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily 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 / Knottin, scorpion toxin-like superfamily / 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 / Chlorotoxin
Similarity search - Component
Biological speciesHomo sapiens (human)
Leiurus quinquestriatus (Egyptian scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBoros, E. / Ecsedi, P. / Szakacs, D. / Nyitray, L.
Funding support Hungary, 1items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)2018-1.2-1-NKP Hungary
CitationJournal: To Be Published
Title: Structure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus)
Authors: Boros, E. / Ecsedi, P. / Szakacs, D. / Nyitray, L.
History
DepositionJan 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
D: Chlorotoxin
C: Chlorotoxin
B: Neuropilin-1


Theoretical massNumber of molelcules
Total (without water)79,8434
Polymers79,8434
Non-polymers00
Water00
1
A: Neuropilin-1
C: Chlorotoxin


Theoretical massNumber of molelcules
Total (without water)39,9212
Polymers39,9212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chlorotoxin
B: Neuropilin-1


Theoretical massNumber of molelcules
Total (without water)39,9212
Polymers39,9212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.880, 194.450, 74.050
Angle α, β, γ (deg.)90.00, 92.33, 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: 35909.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Protein/peptide Chlorotoxin / CTX / ClTx


Mass: 4011.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus (Egyptian scorpion)
Production host: Escherichia coli (E. coli) / References: UniProt: P45639
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: 4.22 Å3/Da / Density % sol: 70.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.04M Potassium phosphate monobasic 16 % w/v PEG 8000 20 % v/v Glycerol (JCSG Plus: D12)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36045 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.888 / Rmerge(I) obs: 0.345 / Rrim(I) all: 0.372 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.7-2.771.16926870.6291.2661
2.77-2.850.87325730.7550.9451
2.85-2.930.65625520.8650.7131
2.93-3.020.50624230.9120.5481
3.02-3.120.40823880.9510.4431
3.12-3.230.33822170.9670.3691
3.23-3.350.23722560.9850.2571
3.35-3.490.20221020.9920.2191
3.49-3.640.20220680.9610.2181
3.64-3.820.22319570.9870.2421
3.82-4.020.22118730.9790.241
4.02-4.270.26417890.9390.2851
4.27-4.560.25116220.9520.2711
4.56-4.930.26815260.8030.2911
4.93-5.40.30714410.9850.331
5.4-6.040.32512970.980.3491
6.04-6.970.39611380.9840.4261
6.97-8.540.3979610.9250.431
8.54-12.070.417560.740.4441
12.07-500.484190.8180.5151

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QQI,6ATW

2qqi

6atw


Resolution: 2.7→48.754 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3138 1797 4.99 %
Rwork0.2627 --
obs0.2649 35993 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 0 0 5188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035325
X-RAY DIFFRACTIONf_angle_d0.7077203
X-RAY DIFFRACTIONf_dihedral_angle_d7.824302
X-RAY DIFFRACTIONf_chiral_restr0.051764
X-RAY DIFFRACTIONf_plane_restr0.004933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.35441390.30052643X-RAY DIFFRACTION100
2.773-2.85460.33951380.30232629X-RAY DIFFRACTION100
2.8546-2.94680.3391380.30232644X-RAY DIFFRACTION100
2.9468-3.05210.31471360.2922593X-RAY DIFFRACTION99
3.0521-3.17420.36131380.29582625X-RAY DIFFRACTION99
3.1742-3.31870.35491350.28322585X-RAY DIFFRACTION97
3.3187-3.49360.33741360.27672602X-RAY DIFFRACTION100
3.4936-3.71240.33111410.26092676X-RAY DIFFRACTION100
3.7124-3.99890.31251380.25272620X-RAY DIFFRACTION100
3.9989-4.40110.32281380.24952628X-RAY DIFFRACTION99
4.4011-5.03740.27781380.22732626X-RAY DIFFRACTION99
5.0374-6.34440.27881400.26472655X-RAY DIFFRACTION100
6.3444-48.750.3181420.26852670X-RAY DIFFRACTION99
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)
13.98152.03282.54995.54142.95585.64970.02390.0925-0.42490.0752-0.12730.18540.7033-0.47550.07360.6181-0.16690.10070.4785-0.03370.51114.5075-34.27373.343
22.84550.26110.99468.70551.08155.28380.08710.2330.4944-0.37720.00390.3934-0.25980.0666-0.01420.3865-0.05610.04130.6065-0.03360.418823.4821-2.467714.4223
33.36931.04651.80156.35921.39285.9688-0.09170.1168-0.1271-0.0620.146-0.5790.3230.2073-0.16490.2944-0.01770.0510.49560.00440.474230.6645-9.031318.6531
44.66590.9920.27065.8711.91521.6171-0.14820.0458-0.4049-0.52850.0534-0.50560.22620.1143-0.10650.4199-0.08870.010.50620.0440.583228.4955-6.430514.3215
54.05410.86845.68110.85171.7548.37921.60150.8045-0.6918-0.8153-0.0867-2.36190.89660.8714-1.38951.4215-0.09130.29590.58810.12831.653929.1103-45.408514.9004
65.2202-6.8652-1.57529.02762.05261.2711-0.2222-0.17371.05191.2906-1.4085-1.98670.38441.28041.44241.0380.0185-0.41421.2660.27841.824530.3712-44.358923.3914
79.7395-5.2978-2.34766.2233-0.94852.0439-0.2547-0.5654-2.7622-0.3353-0.10650.8819-0.58330.29370.15691.0918-0.3291-0.1830.81570.32021.260323.154-45.870122.9402
80.7919-0.2236-0.93490.1528-0.12322.7597-0.2038-0.6921.35670.0412-0.46140.90870.0926-1.11660.61421.8942-0.2756-0.31780.9679-0.27231.4361-3.001-45.0788-23.7871
94.05191.18572.30232.6779-0.8962.36641.2112-0.93182.09870.6174-1.45540.8329-0.7948-0.46970.00111.2159-0.28080.45631.1255-0.55331.4365-5.4714-45.3929-16.4745
109.49917.4471-5.32966.929-5.59214.8234-1.3535-0.38820.5841-0.5385-0.10640.4381-1.0404-0.73941.48081.6073-0.4091-0.29950.8533-0.18460.9839-3.9776-45.9283-9.0724
111.4739-1.7052-1.93181.97312.2342.5259-0.8781-0.00520.4683-1.3664-0.12960.0024-1.54340.00990.67291.7665-0.63210.050.7961-0.31140.56933.6593-42.6045-18.611
123.06543.5323-3.59364.1655-4.23614.31420.1476-1.1559-0.0446-1.11820.35841.29551.2708-0.2573-0.48670.9759-0.29070.06820.935-0.11780.93744.1365-46.807-14.7133
134.64993.3636-2.93565.7548-2.24374.55580.3336-0.349-0.15460.4917-0.4956-0.577-0.8660.62420.17260.7917-0.1489-0.18710.48560.05360.57338.6585-56.05939.49
141.4580.9978-1.65495.8249-0.16774.9088-0.034-0.04290.2365-0.16840.09440.2216-0.3233-0.0780.02090.3656-0.0792-0.15190.56660.06650.7678-7.2624-83.639251.3898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 274 through 428 )
2X-RAY DIFFRACTION2chain 'A' and (resid 429 through 484 )
3X-RAY DIFFRACTION3chain 'A' and (resid 485 through 560 )
4X-RAY DIFFRACTION4chain 'A' and (resid 561 through 583 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 12 )
6X-RAY DIFFRACTION6chain 'D' and (resid 13 through 20 )
7X-RAY DIFFRACTION7chain 'D' and (resid 21 through 36 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'C' and (resid 20 through 25 )
11X-RAY DIFFRACTION11chain 'C' and (resid 26 through 31 )
12X-RAY DIFFRACTION12chain 'C' and (resid 32 through 36 )
13X-RAY DIFFRACTION13chain 'B' and (resid 274 through 425 )
14X-RAY DIFFRACTION14chain 'B' and (resid 426 through 583 )

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