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- PDB-5o0n: Deglycosylated Nogo Receptor with native disulfide structure 4 -

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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 / positive regulation of GTPase activity / axonal growth cone / axonogenesis / dendritic shaft / heparin binding / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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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: 2.6 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.

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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

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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 )

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