[English] 日本語
Yorodumi
- PDB-5o0n: Deglycosylated Nogo Receptor with native disulfide structure 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o0n
TitleDeglycosylated Nogo Receptor with native disulfide structure 4
ComponentsReticulon-4 receptor
KeywordsSIGNALING PROTEIN / nervous system / signaling / leucine-rich repeat domain / disulfide structure
Function / homology
Function and homology information


neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / negative regulation of axon regeneration / ganglioside GT1b binding / negative regulation of axon extension / corpus callosum development / regulation of synapse assembly / positive regulation of Rho protein signal transduction ...neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / negative regulation of axon regeneration / ganglioside GT1b binding / negative regulation of axon extension / corpus callosum development / regulation of synapse assembly / positive regulation of Rho protein signal transduction / regulation of postsynapse assembly / axonal growth cone / positive regulation of GTPase activity / axonogenesis / dendritic shaft / heparin binding / presynapse / negative regulation of neuron projection development / growth cone / perikaryon / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / neuronal cell body / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
: / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Reticulon-4 receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWOVidi 723.012.002 Netherlands
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction.
Authors: Pronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3286
Polymers36,0111
Non-polymers2,3175
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint13 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 90.630, 45.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Reticulon-4 receptor / Nogo receptor / NgR / Nogo-66 receptor / Nogo66 receptor-1 / NgR1


Mass: 36011.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rtn4r, Ngr1, Nogor / Plasmid: pUPE107.03 / Details (production host): secretion signal peptide, / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): GntI-/- / References: UniProt: Q99PI8

-
Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 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.: 1
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

-
Non-polymers , 2 types, 8 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM ...Details: Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM HEPES pH 7.0 at a concentration of 3.3 mg/mL and mixed in a 1:1 molar ratio with Endo-Hf-deglycosylated NgRa at a concentration of 10 mg/mL. Crystals were grown in a condition of 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→90.63 Å / Num. obs: 13084 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rsym value: 0.066 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.704 / Rsym value: 0.912 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZN

1ozn


Resolution: 2.5→90.63 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2
RfactorNum. reflection% reflection
Rfree0.2479 650 4.98 %
Rwork0.2186 --
obs0.2201 13057 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→90.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 152 6 2577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042646
X-RAY DIFFRACTIONf_angle_d1.1233627
X-RAY DIFFRACTIONf_dihedral_angle_d19.41016
X-RAY DIFFRACTIONf_chiral_restr0.052440
X-RAY DIFFRACTIONf_plane_restr0.003454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.69320.34421350.30512450X-RAY DIFFRACTION100
2.6932-2.96430.39911280.31222456X-RAY DIFFRACTION100
2.9643-3.39330.43541240.30472465X-RAY DIFFRACTION100
3.3933-4.27520.24291200.2212495X-RAY DIFFRACTION100
4.2752-90.68960.18941430.17872541X-RAY DIFFRACTION100
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)
18.4836-2.73530.07238.2995-0.74768.27260.3755-0.0344-1.59890.2664-0.1711.20771.4662-0.7199-0.26360.8552-0.1286-0.04420.7276-0.14311.220415.90840.780731.3059
28.2779-3.14480.57497.8336-0.37848.43550.42610.1283-0.57720.446-0.20010.97920.6107-0.6846-0.16730.4961-0.05350.03130.5405-0.11120.840814.778512.567931.9025
31.5928-1.71041.20268.3472-3.8919.26560.39710.4089-0.09520.0848-0.32080.2577-0.3766-0.0448-0.08770.44780.0520.05750.6656-0.13230.568918.427731.582122.4366
47.9659-2.2852-1.40988.8558-2.78126.89970.82011.1172-0.1102-1.4245-0.9985-0.43380.03361.12440.20460.98830.19110.1011.2315-0.02510.577322.880743.71244.8091
59.7159-1.0796-1.39896.0071-1.77727.7663-0.15242.30670.0666-2.75480.18290.036-0.27090.0535-0.06691.73270.36020.10051.62420.06710.802618.767148.9353-5.9321
63.9744-4.50742.55686.4548-5.45182.203-0.00611.2835-0.0876-0.696-0.36580.2205-0.00340.55210.28980.9544-0.0909-0.09910.94550.01660.9818.524861.8074.4614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 290 )
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 308 )
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 339 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more