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- PDB-8tsm: Crystal structure of chicken Netrin-1 LN LE1-2 -

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Basic information

Entry
Database: PDB / ID: 8tsm
TitleCrystal structure of chicken Netrin-1 LN LE1-2
ComponentsNetrin-1
KeywordsSIGNALING PROTEIN / Extracellular matrix protein / apoptosis / axon guidance / neuronal development / cell signaling / heparan sulfate binding protein / dependence receptors
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / tissue development / motor neuron migration / 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 / tissue development / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension / motor neuron axon guidance / nuclear migration / inner ear morphogenesis / positive regulation of cell motility / regulation of synapse assembly / dendrite development / basement membrane / positive regulation of axon extension / glial cell proliferation / positive regulation of glial cell proliferation / animal organ morphogenesis / cell periphery / cell-cell adhesion / actin cytoskeleton / Ras protein signal transduction / glutamatergic synapse / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsHeide, F. / Rafiei, F. / Stetefeld, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Investigation of the dynamic nature of Netrin-1 on dependence receptor signaling
Authors: Rafiei, F. / Heide, F. / Legare, S. / Gabir, H. / Padilla-Meier, P. / Meier, M. / Koch, M. / Stetefeld, J.
History
DepositionAug 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6823
Polymers44,2401
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.413, 112.413, 242.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Netrin-1


Mass: 44239.742 Da / Num. of mol.: 1 / Fragment: residues 26-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTN1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q90922
#2: 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: isolated from a genetically manipulated source
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 interestN
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: 4.75 Å3/Da / Density % sol: 74.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.9→37.77 Å / Num. obs: 13196 / % possible obs: 97.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 155.68 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0705 / Net I/σ(I): 7
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 1682 / CC1/2: 0.705 / Rpim(I) all: 1.268 / % possible all: 96.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.20.1-4487_4487phasing
PHENIX1.20.1-4487_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→37.77 Å / SU ML: 0.5595 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.8442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3191 1041 7.89 %
Rwork0.3119 12155 -
obs0.3124 13196 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 216.96 Å2
Refinement stepCycle: LAST / Resolution: 3.9→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 28 0 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062920
X-RAY DIFFRACTIONf_angle_d0.92963950
X-RAY DIFFRACTIONf_chiral_restr0.0538416
X-RAY DIFFRACTIONf_plane_restr0.0348519
X-RAY DIFFRACTIONf_dihedral_angle_d8.3184406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.110.42241280.48621682X-RAY DIFFRACTION94.27
4.11-4.360.40151460.4261738X-RAY DIFFRACTION97.82
4.36-4.70.36451650.38561705X-RAY DIFFRACTION96.64
4.7-5.170.34291750.36191707X-RAY DIFFRACTION97.01
5.17-5.910.39231570.34791754X-RAY DIFFRACTION98.81
5.92-7.430.3411280.32921784X-RAY DIFFRACTION98.96
7.45-37.770.2431420.23291785X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: 9.41483616592 Å / Origin y: -33.8144231617 Å / Origin z: -19.7101355974 Å
111213212223313233
T1.19535150385 Å20.0700943270092 Å20.0406529633696 Å2-1.35626229749 Å2-0.0539982203077 Å2--1.01464704034 Å2
L0.274839918497 °20.0881311955318 °20.239957189067 °2-0.879420208658 °2-0.289697060531 °2--0.816261168362 °2
S-0.0616574315017 Å °-0.394104884716 Å °0.0213778923593 Å °-0.0212765952714 Å °-0.11409477675 Å °0.151837838789 Å °0.0611693973094 Å °0.043220612911 Å °-0.188339678909 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 40 through 405)

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