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- PDB-6fkq: THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A... -

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Basic information

Entry
Database: PDB / ID: 6fkq
TitleTHE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN
Components
  • Draxin
  • Netrin-1
KeywordsSIGNALING PROTEIN / AXON GUIDANCE CUE / NETRIN-1 / DRAXIN / COMMISSURAL NEURON
Function / homology
Function and homology information


commissural neuron differentiation in spinal cord / dorsal spinal cord development / anterior commissure morphogenesis / regulation of glial cell migration / DSCAM interactions / chemorepulsion of axon / negative regulation of hippocampal neuron apoptotic process / Cdc42 protein signal transduction / anterior/posterior axon guidance / hippocampal neuron apoptotic process ...commissural neuron differentiation in spinal cord / dorsal spinal cord development / anterior commissure morphogenesis / regulation of glial cell migration / DSCAM interactions / chemorepulsion of axon / negative regulation of hippocampal neuron apoptotic process / Cdc42 protein signal transduction / anterior/posterior axon guidance / hippocampal neuron apoptotic process / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / motor neuron migration / negative regulation of axon extension / Netrin mediated repulsion signals / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis / DCC mediated attractive signaling / inner ear morphogenesis / nuclear migration / positive regulation of cell motility / regulation of synapse assembly / basement membrane / positive regulation of axon extension / glial cell proliferation / forebrain development / positive regulation of glial cell proliferation / axon guidance / negative regulation of canonical Wnt signaling pathway / cell-cell adhesion / Wnt signaling pathway / actin cytoskeleton / molecular adaptor activity / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / regulation of transcription by RNA polymerase II / glutamatergic synapse / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Draxin / Draxin / 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 ...Draxin / Draxin / 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
triacetyl-beta-chitotriose / Netrin-1 / Draxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsBhowmick, T. / Meijers, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Marie Curie CoFUND Germany
CitationJournal: Neuron / Year: 2018
Title: Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC.
Authors: Ying Liu / Tuhin Bhowmick / Yiqiong Liu / Xuefan Gao / Haydyn D T Mertens / Dmitri I Svergun / Junyu Xiao / Yan Zhang / Jia-Huai Wang / Rob Meijers /
Abstract: Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue ...Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. VIDEO ABSTRACT.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,70017
Polymers49,1302
Non-polymers2,56915
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-98 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.794, 130.794, 183.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Netrin-1 / Epididymis tissue protein Li 131P


Mass: 46827.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NETRIN-1 IS A PROTOTYPICAL AXON GUIDANCE CUE THAT BINDS TO THE RECEPTOR DELETED IN COLORECTAL CANCER (DCC).
Source: (gene. exp.) Homo sapiens (human) / Gene: NTN1, NTN1L / Plasmid: PXLG / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: O95631
#2: Protein/peptide Draxin / Dorsal inhibitory axon guidance protein / Dorsal repulsive axon guidance protein / Neucrin


Mass: 2302.597 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 225-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DRAXIN, C1orf187, PSEC0258, UNQ3119/PRO10268 / Plasmid: PXLG / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: Q8NBI3

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Sugars , 2 types, 3 molecules

#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 4.62 Å3/Da / Density % sol: 73.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.6 M AMMONIUM SULPHATE AND 0.1 M SODIUM CITRATE, AT PH 4 TO PH 5, VAPOR DIFFUSION, TEMPERATURE 298K
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.07→54.13 Å / Num. obs: 18063 / % possible obs: 99.9 % / Redundancy: 32.9 % / Rmerge(I) obs: 0.587 / Net I/σ(I): 8.7
Reflection shellResolution: 3.07→3.23 Å / Redundancy: 18.6 % / Rmerge(I) obs: 2.897 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
Aimless3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4URT

4urt


Resolution: 3.07→54.01 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU B: 23.425 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R: 0.826 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 874 4.9 %RANDOM
Rwork0.235 ---
obs0.237 17128 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å21.21 Å20 Å2
2--2.42 Å20 Å2
3----7.84 Å2
Refinement stepCycle: LAST / Resolution: 3.07→54.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 155 0 3575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193684
X-RAY DIFFRACTIONr_bond_other_d0.010.023250
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9824993
X-RAY DIFFRACTIONr_angle_other_deg1.74437507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0035432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40522.753178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031537
X-RAY DIFFRACTIONr_chiral_restr0.0940.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214087
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02874
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3947.3341736
X-RAY DIFFRACTIONr_mcbond_other4.3817.3311735
X-RAY DIFFRACTIONr_mcangle_it7.18610.9942164
X-RAY DIFFRACTIONr_mcangle_other7.18510.9982165
X-RAY DIFFRACTIONr_scbond_it4.8877.9871948
X-RAY DIFFRACTIONr_scbond_other4.8867.9871948
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.43611.7892830
X-RAY DIFFRACTIONr_long_range_B_refined11.1687.8383929
X-RAY DIFFRACTIONr_long_range_B_other11.1687.8343929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.07→3.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 63 -
Rwork0.395 1222 -
obs--99.3 %

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