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- PDB-4pln: Crystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mou... -

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Basic information

Entry
Database: PDB / ID: 4pln
TitleCrystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mouse Neogenin (FN4-5)
Components
  • Neogenin
  • Netrin-1
KeywordsPROTEIN BINDING / elongated / cysteine rich / glycoprotein / complex
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / Cdc42 protein signal transduction / anterior/posterior axon guidance / trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / motor neuron migration / co-receptor binding / negative regulation of axon extension / BMP receptor binding ...regulation of glial cell migration / chemorepulsion of axon / Cdc42 protein signal transduction / anterior/posterior axon guidance / trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / motor neuron migration / co-receptor binding / negative regulation of axon extension / BMP receptor binding / substrate-dependent cell migration, cell extension / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / positive regulation of cell motility / inner ear morphogenesis / nuclear migration / regulation of synapse assembly / intracellular vesicle / basement membrane / protein secretion / negative regulation of protein secretion / glial cell proliferation / positive regulation of axon extension / positive regulation of glial cell proliferation / cell periphery / cell-cell adhesion / postsynaptic density membrane / multicellular organismal-level iron ion homeostasis / actin cytoskeleton / signaling receptor activity / growth cone / Ras protein signal transduction / intracellular iron ion homeostasis / cell adhesion / cadherin binding / regulation of DNA-templated transcription / glutamatergic synapse / cell surface / Golgi apparatus / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / : / Laminin/attractin 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. ...Neogenin, C-terminal / Neogenin C-terminus / : / Laminin/attractin 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 / 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 / Jelly Rolls / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
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.d_res_high / _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_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 1.6Dec 27, 2023Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Oct 30, 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-1
C: Neogenin
D: Neogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,01412
Polymers142,6074
Non-polymers1,4078
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-38 kcal/mol
Surface area62650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.070, 130.211, 126.037
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILEchain AAA40 - 45615 - 431
21PROPROILEILEchain BBB40 - 45615 - 431
12GLYGLYGLYGLYchain CCC763 - 9671 - 205
22GLYGLYSERSERchain DDD763 - 9661 - 204

NCS ensembles :
ID
1
2

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Components

#1: Protein Netrin-1


Mass: 48545.699 Da / Num. of mol.: 2 / 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
#2: Protein Neogenin


Mass: 22757.711 Da / Num. of mol.: 2 / Fragment: FN4-5 (UNP residues 765-964) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97798
#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.: 6 / 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Hepes pH 7.0, 12% PEG3350

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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: 3.2→50 Å / Num. obs: 40756 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 60.75 Å2 / Rmerge(I) obs: 0.2 / Χ2: 0.571 / Net I/av σ(I): 4.538 / Net I/σ(I): 2.6 / Num. measured all: 154909
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.313.50.89640880.43897.8
3.31-3.453.70.69640540.4798.4
3.45-3.63.80.51740800.48798.3
3.6-3.793.60.38939890.54296.2
3.79-4.033.90.30940920.53998.4
4.03-4.3440.21540980.57198.8
4.34-4.783.90.15440770.62498.1
4.78-5.473.90.13840260.58596.5
5.47-6.893.90.13341290.60198.6
6.89-503.80.07141230.82296.7

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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
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.949 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2000 4.91 %
Rwork0.196 --
obs0.1981 40730 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 3.2→49.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9740 0 86 0 9826
Biso mean--63.92 --
Num. residues----1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710116
X-RAY DIFFRACTIONf_angle_d1.17313705
X-RAY DIFFRACTIONf_dihedral_angle_d14.3743731
X-RAY DIFFRACTIONf_chiral_restr0.0481490
X-RAY DIFFRACTIONf_plane_restr0.0071787
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3663X-RAY DIFFRACTION15.828TORSIONAL
12B3663X-RAY DIFFRACTION15.828TORSIONAL
21C1795X-RAY DIFFRACTION15.828TORSIONAL
22D1795X-RAY DIFFRACTION15.828TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27190.36851310.32662539X-RAY DIFFRACTION90
3.2719-3.36030.38861450.28492802X-RAY DIFFRACTION98
3.3603-3.45920.3021430.25952782X-RAY DIFFRACTION98
3.4592-3.57080.31291430.24632771X-RAY DIFFRACTION98
3.5708-3.69840.28371440.22972787X-RAY DIFFRACTION98
3.6984-3.84640.30021390.21052683X-RAY DIFFRACTION95
3.8464-4.02140.23231450.19812822X-RAY DIFFRACTION99
4.0214-4.23330.19761440.17282775X-RAY DIFFRACTION99
4.2333-4.49840.19631460.15352831X-RAY DIFFRACTION99
4.4984-4.84550.17851420.13872760X-RAY DIFFRACTION98
4.8455-5.33260.19121420.15472737X-RAY DIFFRACTION96
5.3326-6.10310.22221460.17052829X-RAY DIFFRACTION99
6.1031-7.68470.20971420.19112765X-RAY DIFFRACTION97
7.6847-49.95520.21681480.19312847X-RAY DIFFRACTION98

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