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- PDB-4plo: Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mo... -

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Basic information

Entry
Database: PDB / ID: 4plo
TitleCrystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)
Components
  • Netrin receptor DCC
  • Netrin-1
KeywordsPROTEIN BINDING / elongated / complex
Function / homology
Function and homology information


Caspase activation via Dependence Receptors in the absence of ligand / Netrin-1 signaling / DCC mediated attractive signaling / regulation of glial cell migration / dorsal/ventral axon guidance / chemorepulsion of axon / Cdc42 protein signal transduction / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / motor neuron migration ...Caspase activation via Dependence Receptors in the absence of ligand / Netrin-1 signaling / DCC mediated attractive signaling / regulation of glial cell migration / dorsal/ventral axon guidance / chemorepulsion of axon / Cdc42 protein signal transduction / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension / 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 / cell periphery / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cell-cell adhesion / neuron migration / actin cytoskeleton / Ras protein signal transduction / axon / apoptotic process / glutamatergic synapse / 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 / Immunoglobulin domain / 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 receptor DCC / Netrin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.901 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 1.2Sep 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 / entity_src_nat / 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 / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 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 1.5Dec 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
Revision 1.6Nov 20, 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
B: Netrin receptor DCC
A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,49611
Polymers71,3122
Non-polymers1,1849
Water1,29772
1
B: Netrin receptor DCC
A: Netrin-1
hetero molecules

B: Netrin receptor DCC
A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,99222
Polymers142,6244
Non-polymers2,36818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Unit cell
Length a, b, c (Å)49.478, 72.939, 285.159
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 BA

#1: Protein Netrin receptor DCC / Tumor suppressor protein DCC


Mass: 22766.400 Da / Num. of mol.: 1 / Fragment: FN4-4 (UNP residues 721-922) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P70211
#2: 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: Homo sapiens (human) / References: UniProt: Q90922

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Sugars , 1 types, 3 molecules

#3: 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 , 3 types, 78 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22875 / % possible obs: 96.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 68.74 Å2 / Rmerge(I) obs: 0.113 / Χ2: 1.042 / Net I/av σ(I): 12.417 / Net I/σ(I): 5.8 / Num. measured all: 93328
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-2.953.10.8829750.70785.5
2.95-33.30.89210030.77587.4
3-3.063.50.73110920.75292.7
3.06-3.123.80.66210760.77292.7
3.12-3.1940.61110980.80995.4
3.19-3.274.10.44211170.83994.3
3.27-3.354.10.40811210.83795.8
3.35-3.443.90.34410830.85694.2
3.44-3.544.10.24511580.92996.4
3.54-3.654.50.22511570.95599.3
3.65-3.784.50.18911760.91999.5
3.78-3.944.40.16311691.05299.8
3.94-4.114.30.12711991.074100
4.11-4.334.30.09911691.15799.6
4.33-4.63.90.07911751.36397.1
4.6-4.964.50.07611931.32199.5
4.96-5.464.50.07312081.23499.6
5.46-6.244.30.06912021.20599.3
6.24-7.864.10.05612031.22197.1
7.86-5040.03813011.54595.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.901→48.75 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1995 8.76 %
Rwork0.2235 --
obs0.2291 22776 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.901→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 68 72 4868
Biso mean--51.65 31.12 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094926
X-RAY DIFFRACTIONf_angle_d1.4146665
X-RAY DIFFRACTIONf_dihedral_angle_d17.341804
X-RAY DIFFRACTIONf_chiral_restr0.112722
X-RAY DIFFRACTIONf_plane_restr0.008862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.97390.38571170.37271227X-RAY DIFFRACTION82
2.9739-3.05430.46771320.32841387X-RAY DIFFRACTION90
3.0543-3.14420.36621380.30481422X-RAY DIFFRACTION93
3.1442-3.24560.34211360.28641419X-RAY DIFFRACTION94
3.2456-3.36160.36061390.24781447X-RAY DIFFRACTION95
3.3616-3.49620.32291390.22911448X-RAY DIFFRACTION94
3.4962-3.65520.27621450.21251510X-RAY DIFFRACTION99
3.6552-3.84790.29531480.21571549X-RAY DIFFRACTION99
3.8479-4.08880.29081470.20481528X-RAY DIFFRACTION100
4.0888-4.40440.26011470.18661535X-RAY DIFFRACTION99
4.4044-4.84720.21821470.16861532X-RAY DIFFRACTION98
4.8472-5.54780.26251510.20341571X-RAY DIFFRACTION99
5.5478-6.98630.27881500.23271555X-RAY DIFFRACTION98
6.9863-48.75650.2771590.23271651X-RAY DIFFRACTION97

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