[English] 日本語
Yorodumi
- PDB-8c5g: Structure of human Neuropilin-1 b1b2 domains in complex with Chlo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c5g
TitleStructure of human Neuropilin-1 b1b2 domains in complex with Chlorotoxin (Leiurus quinquestriatus)
Components
  • Chlorotoxin
  • Neuropilin-1Neuropilin 1
KeywordsTOXIN / Cancer / Co-receptor / protein-protein complex / Teranostic
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 / metalloendopeptidase inhibitor activity / 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 / chloride channel regulator activity / 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 / toxin activity / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry
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) / MAM domain, meprin/A5/mu / MAM domain ...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) / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
1
A: Neuropilin-1
C: Chlorotoxin


  • defined by author
  • Evidence: BLI measurements (OCTET)
  • 39.9 kDa, 2 polymers
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


  • defined by author
  • 39.9 kDa, 2 polymers
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

-
Components

#1: Protein Neuropilin-1 / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more