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- PDB-8snp: Crystal structure of mouse Netrin-1 in complex with samarium ions -

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Basic information

Entry
Database: PDB / ID: 8snp
TitleCrystal structure of mouse Netrin-1 in complex with samarium ions
ComponentsNetrin-1
KeywordsAPOPTOSIS / Extracellular matrix protein / axon guidance / neuronal development / cell signaling
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 / mammary gland development / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis ...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 / mammary gland development / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis / motor neuron axon guidance / nuclear migration / positive regulation of cell motility / inner ear morphogenesis / regulation of synapse assembly / dendrite development / basement membrane / positive regulation of axon extension / glial cell proliferation / positive regulation of glial cell proliferation / regulation of cell migration / axonogenesis / axon guidance / cell periphery / animal organ morphogenesis / neuron migration / cell-cell adhesion / actin cytoskeleton / collagen-containing extracellular matrix / Ras protein signal transduction / cell population proliferation / glutamatergic synapse / synapse / apoptotic process / extracellular region / nucleoplasm / cytosol / cytoplasm
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
SAMARIUM (III) ION / Netrin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHeide, F. / Legare, S. / Stetefeld, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Investigating the structural and functional roles of calcium binding in Netrin-1
Authors: Legare, S. / Heide, F. / Gabir, H. / Rafiei, F. / Meier, M. / Koch, M. / Stetefeld, J.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Assembly

Deposited unit
A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9619
Polymers67,9231
Non-polymers2,0398
Water00
1
A: Netrin-1
hetero molecules

A: Netrin-1
hetero molecules


  • defined by author
  • Evidence: SAXS, Monomer and dimer equilibrium has been reported. (https://doi.org/10.1038/s41467-023-36692-w), gel filtration, https://doi.org/10.1007/s00253-021-11438-0 https://doi.org/10. ...Evidence: SAXS, Monomer and dimer equilibrium has been reported. (https://doi.org/10.1038/s41467-023-36692-w), gel filtration, https://doi.org/10.1007/s00253-021-11438-0 https://doi.org/10.1038/s41467-023-36692-w, assay for oligomerization, Mass photometry experiments confirm a monomer-dimer equilibrium. (https://doi.org/10.1038/s41467-023-36692-w)
  • 140 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)139,92318
Polymers135,8452
Non-polymers4,07816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.500, 69.500, 333.641
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Netrin-1


Mass: 67922.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ntn1 / Production host: Homo sapiens (human) / References: UniProt: O09118
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}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.: 1
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: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Sm / Feature type: SUBJECT OF INVESTIGATION
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 0.1M HEPES pH 7.7, 2.8M NaCl, 0.2M glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0349 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0349 Å / Relative weight: 1
ReflectionResolution: 3.4→66.7 Å / Num. obs: 13728 / % possible obs: 99.35 % / Redundancy: 8.3 % / Biso Wilson estimate: 90.54 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.255 / Net I/σ(I): 5.8
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2782 / CC1/2: 0.923 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→56.62 Å / SU ML: 0.3418 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 614 4.5 %
Rwork0.2496 13039 -
obs0.2505 13653 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.22 Å2
Refinement stepCycle: LAST / Resolution: 3.4→56.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 98 0 3238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583312
X-RAY DIFFRACTIONf_angle_d0.87284497
X-RAY DIFFRACTIONf_chiral_restr0.0459493
X-RAY DIFFRACTIONf_plane_restr0.0417597
X-RAY DIFFRACTIONf_dihedral_angle_d14.6229497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.740.3591360.33253183X-RAY DIFFRACTION98.9
3.74-4.280.28271400.23693190X-RAY DIFFRACTION99.28
4.28-5.40.25861580.23043236X-RAY DIFFRACTION99.65
5.4-56.620.24841800.2413430X-RAY DIFFRACTION99.59
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)
12.353712920060.07956608838250.5665005071120.3318282873970.2167725854053.922318636230.608600247830.139501819524-0.278952893652-0.0107526865828-0.1369535848720.1197285298190.69486735707-0.457153207997-0.3395026492480.9930559001450.0302571405456-0.09682450826850.9614109961370.07363627162140.87070987889434.2326212527-26.9707589726-15.401554724
22.307297604561.009346993341.510051499010.6617250115360.06586802726422.49141740137-0.2858722579910.4633071517590.2511507310430.07368020048850.1663789176240.252242389921-0.5302375304290.4150273146570.1205038270920.7118103376430.12412039229-0.05430001459350.7807911969850.05861284711310.72943929212738.666841207-12.2720404309-17.3625175249
31.18153275355-0.200373219337-0.6036830115741.736535668811.652975162213.443253066630.0541218541520.103275458949-0.04869938070380.38897219209-0.01660850643180.1005296246310.04175273585410.2893009996310.04585602506340.9854660865860.282397484689-0.0206840784380.877134172176.37898479539E-50.85465446547745.0060985756-14.422300495525.8486141437
40.100316675217-0.163320049983-0.2740816354720.2657483858580.4566905515620.708764827017-0.370648930979-0.0861267330729-0.140908278564-0.146217196150.228839571669-0.3382918112151.072499993170.424649316339-0.1296870648661.092724321840.151985728542-0.06021037641941.071455278030.02112474663130.74191295039650.23965518-5.4429080909468.3609910652
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 141 )37 - 1411 - 99
22chain 'A' and (resid 142 through 285 )142 - 285100 - 238
33chain 'A' and (resid 286 through 400 )286 - 400239 - 353
44chain 'A' and (resid 401 through 456 )401 - 456354 - 409

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