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- PDB-4plm: Crystal Structure of Chicken Netrin-1 (LN-LE3) -

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Basic information

Entry
Database: PDB / ID: 4plm
TitleCrystal Structure of Chicken Netrin-1 (LN-LE3)
ComponentsNetrin-1
KeywordsPROTEIN BINDING / elongated / cysteine rich / glycoprotein
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / B cell mediated immunity / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / T cell mediated immunity / substrate-dependent cell migration, cell extension ...regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / B cell mediated immunity / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / T cell mediated immunity / substrate-dependent cell migration, cell extension / motor neuron axon guidance / positive regulation of cell motility / nuclear migration / regulation of synapse assembly / inner ear morphogenesis / B cell proliferation / dendrite development / basement membrane / glial cell proliferation / positive regulation of axon extension / positive regulation of glial cell proliferation / substrate adhesion-dependent cell spreading / cytokine activity / 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 / Netrin C-terminal 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 / Galactose-binding domain-like / EGF-like domain signature 1. / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsXu, K. / Nikolov, D.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Science / Year: 2014
Title: Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism.
Authors: Xu, K. / Wu, Z. / Renier, N. / Antipenko, A. / Tzvetkova-Robev, D. / Xu, Y. / Minchenko, M. / Nardi-Dei, V. / Rajashankar, K.R. / Himanen, J. / Tessier-Lavigne, M. / Nikolov, D.B.
History
DepositionMay 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3458
Polymers48,5461
Non-polymers7997
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Netrin-1
hetero molecules

A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,68916
Polymers97,0912
Non-polymers1,59814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4290 Å2
ΔGint-72 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.627, 62.627, 269.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Netrin-1


Mass: 48545.699 Da / Num. of mol.: 1 / Fragment: LN-LE3 (UNP residues 26-457)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTN1 / Production host: Baculoviridae (virus) / 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.: 3 / 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

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Non-polymers , 4 types, 86 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: NaoAc, NaCacodylate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17693 / % possible obs: 98.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 63.72 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.682 / Net I/av σ(I): 23.281 / Net I/σ(I): 11.3 / Num. measured all: 92454
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.85.117021.39797.8
2.8-2.915.417211.41199.50.734
2.91-3.045.417451.44799.80.522
3.04-3.25.417771.46399.90.335
3.2-3.45.317381.699.90.219
3.4-3.665.417681.65499.70.135
3.66-4.035.317731.86799.60.09
4.03-4.625.217962.02399.80.065
4.62-5.815.218112.06798.90.054
5.81-504.818621.89693.80.036

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
ADSCdata collection
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.801→28.639 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2913 10.08 %
Rwork0.1923 --
obs0.1989 28902 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.801→28.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 46 85 3386
Biso mean--112.41 56.05 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093398
X-RAY DIFFRACTIONf_angle_d1.4014578
X-RAY DIFFRACTIONf_dihedral_angle_d17.1431259
X-RAY DIFFRACTIONf_chiral_restr0.116485
X-RAY DIFFRACTIONf_plane_restr0.008604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.801-2.84650.43151420.33571308X-RAY DIFFRACTION99
2.8465-2.89550.40351300.3111185X-RAY DIFFRACTION99
2.8955-2.94810.37351380.32151242X-RAY DIFFRACTION99
2.9481-3.00470.37881390.29091283X-RAY DIFFRACTION99
3.0047-3.0660.33241330.27931186X-RAY DIFFRACTION99
3.066-3.13260.33311530.26131285X-RAY DIFFRACTION99
3.1326-3.20540.36221350.26661170X-RAY DIFFRACTION100
3.2054-3.28540.30611500.24571270X-RAY DIFFRACTION99
3.2854-3.37410.34291340.21151238X-RAY DIFFRACTION100
3.3741-3.47320.2441460.19391265X-RAY DIFFRACTION100
3.4732-3.58510.25441300.18321205X-RAY DIFFRACTION99
3.5851-3.7130.23031370.17441262X-RAY DIFFRACTION99
3.713-3.86140.27431440.17571244X-RAY DIFFRACTION100
3.8614-4.03660.22831400.17081215X-RAY DIFFRACTION99
4.0366-4.24880.26491390.16221245X-RAY DIFFRACTION99
4.2488-4.51410.20741360.14371271X-RAY DIFFRACTION100
4.5141-4.8610.14931510.13281231X-RAY DIFFRACTION100
4.861-5.34740.20651320.14521226X-RAY DIFFRACTION100
5.3474-6.11460.25011380.16961248X-RAY DIFFRACTION99
6.1146-7.6790.2651400.19651234X-RAY DIFFRACTION99
7.679-28.64030.25071260.20711176X-RAY DIFFRACTION94
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)
12.5748-0.23430.2124.54611.64454.92810.02940.0018-0.5363-0.040.0537-0.12140.4674-0.0698-0.0390.53690.0318-0.03530.4073-0.02790.3736-33.08283.758822.7374
20.03970.07510.59750.71450.8523.13710.04570.1072-0.0858-0.3432-0.0308-0.0765-0.4906-0.04870.04570.5405-0.0283-0.0550.702-0.13720.3855-19.716326.739862.9174
322-5.760324.3712-2.5986-1.87990.5639-1.27772.2659-0.40322.72111.28610.36131.7799-0.3573-0.18431.2725-0.07150.7277-13.282552.9017113.5523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 265 )
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 456 )
3X-RAY DIFFRACTION3chain 'A' and (resid 457 through 457 )

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