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- PDB-7lrf: Netrin-1 in complex with SOS -

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Basic information

Entry
Database: PDB / ID: 7lrf
TitleNetrin-1 in complex with SOS
ComponentsNetrin-1
KeywordsSIGNALING PROTEIN / self assembly / localization / sulfate binding
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / substrate-dependent cell migration, cell extension / motor neuron axon guidance / nuclear migration ...regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / substrate-dependent cell migration, cell extension / motor neuron axon guidance / nuclear migration / positive regulation of cell motility / inner ear morphogenesis / regulation of synapse assembly / dendrite development / basement membrane / glial cell proliferation / positive regulation of axon extension / positive regulation of glial cell proliferation / cell periphery / animal organ morphogenesis / cell-cell adhesion / actin cytoskeleton / Ras protein signal transduction / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain ...Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain signature 1. / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
sucrose octasulfate / DI(HYDROXYETHYL)ETHER / Netrin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsGupta, M. / McDougall, M. / Torres, A.M. / Stetefeld, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)RPA-109759 Canada
CitationJournal: Nat Commun / Year: 2023
Title: The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation.
Authors: Meier, M. / Gupta, M. / Akgul, S. / McDougall, M. / Imhof, T. / Nikodemus, D. / Reuten, R. / Moya-Torres, A. / To, V. / Ferens, F. / Heide, F. / Padilla-Meier, G.P. / Kukura, P. / Huang, W. ...Authors: Meier, M. / Gupta, M. / Akgul, S. / McDougall, M. / Imhof, T. / Nikodemus, D. / Reuten, R. / Moya-Torres, A. / To, V. / Ferens, F. / Heide, F. / Padilla-Meier, G.P. / Kukura, P. / Huang, W. / Gerisch, B. / Morgelin, M. / Poole, K. / Antebi, A. / Koch, M. / Stetefeld, J.
History
DepositionFeb 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin-1
B: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,48923
Polymers99,1602
Non-polymers6,32921
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.105, 80.152, 241.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Netrin-1


Mass: 49579.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTN1 / Production host: Homo sapiens (human) / References: UniProt: Q90922

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Sugars , 3 types, 10 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf3SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO36SO3]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 53 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG 8000, 100 mM CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54192 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54192 Å / Relative weight: 1
ReflectionResolution: 3.208→35.36 Å / Num. obs: 24533 / % possible obs: 99.33 % / Redundancy: 8.3 % / Biso Wilson estimate: 81.46 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.102 / Rrim(I) all: 0.172 / Χ2: 0.98 / Net I/σ(I): 9.3
Reflection shellResolution: 3.21→3.43 Å / Num. unique obs: 2351 / CC1/2: 0.634

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OVE

4ove


Resolution: 3.21→35.357 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1191 4.86 %
Rwork0.2264 23340 -
obs0.2291 24531 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 305.08 Å2 / Biso mean: 92.3585 Å2 / Biso min: 31.29 Å2
Refinement stepCycle: final / Resolution: 3.21→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 422 42 6765
Biso mean--150.34 57.2 -
Num. residues----829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.21-3.340.40761060.32092523262998
3.34-3.490.35891260.300925472673100
3.49-3.670.38231360.287725602696100
3.67-3.90.33571340.262925672701100
3.9-4.20.27391580.228425712729100
4.2-4.620.2321290.180625722701100
4.62-5.290.2271270.175226292756100
5.29-6.660.30531400.220326402780100
6.66-35.360.23341350.20882731286698
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)
17.18090.21622.80013.25330.19234.44020.3007-0.8425-0.35730.2239-0.078-0.83830.2222-0.0212-0.13290.3508-0.05480.01030.46680.03430.648457.66244.994898.1574
21.95461.10313.53110.14491.57678.1119-0.0688-0.0834-0.0781-0.18590.21320.0054-0.3515-0.2399-0.05380.6668-0.006-0.06090.3833-0.06140.642125.9852-1.012852.1288
30.18890.7312.20614.26614.94948.7621-0.11080.3962-0.1581-0.26460.4146-0.16060.12541.0088-0.57250.4076-0.10470.11620.9021-0.01480.791518.6355-20.3256-39.9787
41.63730.5358-0.26232.43411.63374.4687-0.00450.014-0.4270.17470.0717-0.18030.67130.4332-0.08990.4180.1079-0.18940.42430.07170.73929.9234-24.6092-30.7257
51.0211-0.28512.39921.0319-0.05256.069-0.54820.42450.2224-0.01710.1457-0.051-1.47310.06220.3030.8728-0.1824-0.0910.553-0.06180.639821.77135.285520.1676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 40 through 295 )B40 - 295
2X-RAY DIFFRACTION2chain 'B' and (resid 296 through 457 )B296 - 457
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 115 )A40 - 115
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 321 )A116 - 321
5X-RAY DIFFRACTION5chain 'A' and (resid 322 through 457 )A322 - 457

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