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- PDB-4urt: The crystal structure of a fragment of netrin-1 in complex with F... -

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Basic information

Entry
Database: PDB / ID: 4urt
TitleThe crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC
Components
  • NETRIN RECEPTOR DCC
  • NETRIN-1
KeywordsPROTEIN BINDING / APOPTOSIS / AXON GUIDANCE / DEPENDENCE RECEPTOR
Function / homology
Function and homology information


regulation of glial cell migration / dorsal/ventral axon guidance / DSCAM interactions / chemorepulsion of axon / Cdc42 protein signal transduction / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / negative regulation of dendrite development ...regulation of glial cell migration / dorsal/ventral axon guidance / DSCAM interactions / chemorepulsion of axon / Cdc42 protein signal transduction / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / negative regulation of dendrite development / 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 / Caspase activation via Dependence Receptors in the absence of ligand / 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 / postsynaptic modulation of chemical synaptic transmission / glial cell proliferation / positive regulation of glial cell proliferation / axonogenesis / axon guidance / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cell-cell adhesion / neuron migration / transmembrane signaling receptor activity / actin cytoskeleton / negative regulation of neuron projection development / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / apoptotic process / regulation of transcription by RNA polymerase II / glutamatergic synapse / cell surface / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / 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 ...Neogenin, C-terminal / Neogenin C-terminus / 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Netrin-1 / Netrin receptor DCC
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFinci, L.I. / Krueger, N. / Sun, X. / Zhang, J. / Chegkazi, M. / Wu, Y. / Schenk, G. / Mertens, H.D.T. / Svergun, D.I. / Zhang, Y. ...Finci, L.I. / Krueger, N. / Sun, X. / Zhang, J. / Chegkazi, M. / Wu, Y. / Schenk, G. / Mertens, H.D.T. / Svergun, D.I. / Zhang, Y. / Wang, J.-h. / Meijers, R.
CitationJournal: Neuron / Year: 2014
Title: The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.
Authors: Lorenzo I Finci / Nina Krüger / Xiaqin Sun / Jie Zhang / Magda Chegkazi / Yu Wu / Gundolf Schenk / Haydyn D T Mertens / Dmitri I Svergun / Yan Zhang / Jia-Huai Wang / Rob Meijers /
Abstract: Netrin-1 is a guidance cue that can trigger either attraction or repulsion effects on migrating axons of neurons, depending on the repertoire of receptors available on the growth cone. How a single ...Netrin-1 is a guidance cue that can trigger either attraction or repulsion effects on migrating axons of neurons, depending on the repertoire of receptors available on the growth cone. How a single chemotropic molecule can act in such contradictory ways has long been a puzzle at the molecular level. Here we present the crystal structure of netrin-1 in complex with the Deleted in Colorectal Cancer (DCC) receptor. We show that one netrin-1 molecule can simultaneously bind to two DCC molecules through a DCC-specific site and through a unique generic receptor binding site, where sulfate ions staple together positively charged patches on both DCC and netrin-1. Furthermore, we demonstrate that UNC5A can replace DCC on the generic receptor binding site to switch the response from attraction to repulsion. We propose that the modularity of binding allows for the association of other netrin receptors at the generic binding site, eliciting alternative turning responses.
History
DepositionJul 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Data collection / Version format compliance
Revision 1.2Dec 2, 2015Group: Derived calculations
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NETRIN-1
B: NETRIN RECEPTOR DCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,80225
Polymers70,7282
Non-polymers3,07423
Water00
1
B: NETRIN RECEPTOR DCC
hetero molecules

A: NETRIN-1
B: NETRIN RECEPTOR DCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,23428
Polymers93,9723
Non-polymers3,26225
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_554-x,y+1/2,-z-1/21
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-225 kcal/mol
Surface area35660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 87.410, 155.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NETRIN-1 / EPIDIDYMIS TISSUE PROTEIN LI 131P


Mass: 47484.527 Da / Num. of mol.: 1 / Fragment: VI AND V DOMAINS, RESIDUES 39-453 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O95631
#2: Protein NETRIN RECEPTOR DCC / COLORECTAL CANCER SUPPRESSOR / IMMUNOGLOBULIN SUPERFAMILY DCC SUBCLASS MEMBER 1 / TUMOR SUPPRESSOR ...COLORECTAL CANCER SUPPRESSOR / IMMUNOGLOBULIN SUPERFAMILY DCC SUBCLASS MEMBER 1 / TUMOR SUPPRESSOR PROTEIN DCC / DELETED IN COLORECTAL CANCER


Mass: 23243.568 Da / Num. of mol.: 1 / Fragment: FN5-FN6, RESIDUES 844-1043 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P43146

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Sugars , 1 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.: 3
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

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Non-polymers , 4 types, 20 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / 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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Details

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: 2 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6
Details: 0.1M MES PH 6.0, 0.15M AMMONIUM SULFATE AND 15% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2013 / Details: KB MIRRORS
RadiationMonochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 20291 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.8
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQT

4aqt


Resolution: 3.1→77.659 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 1095 5.1 %
Rwork0.2297 --
obs0.2314 20291 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→77.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 177 0 5118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0215267
X-RAY DIFFRACTIONf_angle_d0.8637124
X-RAY DIFFRACTIONf_dihedral_angle_d11.0261918
X-RAY DIFFRACTIONf_chiral_restr0.121767
X-RAY DIFFRACTIONf_plane_restr0.003915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.24110.33641270.29372397X-RAY DIFFRACTION95
3.2411-3.4120.30061410.26112446X-RAY DIFFRACTION99
3.412-3.62570.29961360.25232523X-RAY DIFFRACTION100
3.6257-3.90570.25171540.23742506X-RAY DIFFRACTION100
3.9057-4.29870.27851280.2142552X-RAY DIFFRACTION100
4.2987-4.92060.2411380.1992559X-RAY DIFFRACTION100
4.9206-6.19910.27791470.22032582X-RAY DIFFRACTION100
6.1991-77.68280.23671240.23372726X-RAY DIFFRACTION100

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