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- PDB-5o0l: Deglycosylated Nogo Receptor with native disulfide structure 2 -

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Basic information

Entry
Database: PDB / ID: 5o0l
TitleDeglycosylated Nogo Receptor with native disulfide structure 2
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: 2.511 Å
AuthorsPronker, M.F. / 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 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 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 1.6Nov 6, 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
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,45611
Polymers72,0222
Non-polymers1,4349
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-7 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.909, 38.597, 119.610
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36011.207 Da / Num. of mol.: 2
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, C-terminal His6
Cell line (production host): HEK293 GntI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q99PI8
#2: 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: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Result of a co-crystallization trial with the Endo-Hf-deglycosylated extracellular domain of mouse MAG (UNIPROT P20917, residues 20-508) in SEC buffer, mixed at equimolar stoichiometry. NgRa ...Details: Result of a co-crystallization trial with the Endo-Hf-deglycosylated extracellular domain of mouse MAG (UNIPROT P20917, residues 20-508) in SEC buffer, mixed at equimolar stoichiometry. NgRa was also Endo-Hf-deglycosylated. Crystals were grown in a condition of 0.5 M LiCl, 0.05 M citric acid pH 4.0, 15 % (w/v) PEG6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→38.6 Å / Num. obs: 20826 / % possible obs: 94.6 % / Redundancy: 2.8 % / CC1/2: 0.992 / Rsym value: 0.099 / Net I/σ(I): 12.2
Reflection shellResolution: 2.51→2.62 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.3 / CC1/2: 0.564 / Rsym value: 0.561 / % possible all: 89.6

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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: 2.511→38.404 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.256 1009 4.87 %
Rwork0.1968 --
obs0.1996 20717 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.511→38.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 87 119 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024776
X-RAY DIFFRACTIONf_angle_d0.5216518
X-RAY DIFFRACTIONf_dihedral_angle_d14.7251778
X-RAY DIFFRACTIONf_chiral_restr0.042743
X-RAY DIFFRACTIONf_plane_restr0.004847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.511-2.64340.34661460.28142674X-RAY DIFFRACTION89
2.6434-2.8090.32371630.25372859X-RAY DIFFRACTION96
2.809-3.02580.27981570.23392886X-RAY DIFFRACTION95
3.0258-3.33010.29381430.22232842X-RAY DIFFRACTION94
3.3301-3.81160.23791440.18142824X-RAY DIFFRACTION93
3.8116-4.80070.21341290.15162798X-RAY DIFFRACTION91
4.8007-38.40850.21841270.1822825X-RAY DIFFRACTION88
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)
13.9425-0.97320.39956.9909-0.43464.67060.29740.50820.0176-0.2856-0.2938-0.5554-0.1560.7587-0.00920.1760.02340.07690.38880.04330.406152.285317.602352.4027
26.284-0.2941-1.04152.990.1723.7230.17290.29110.2267-0.1155-0.05-0.1305-0.21470.0189-0.13320.1396-0.00040.00460.16030.04520.197736.78621.357557.1616
36.0993-2.7312-0.66696.27950.25745.1977-0.0472-0.1752-0.1741-0.02770.22320.151-0.4808-0.2377-0.170.1561-0.01230.02630.16030.0430.197926.304722.027868.1758
45.4225-0.22860.94393.79061.10196.9603-0.108-0.285-0.10670.25860.15210.4286-0.1943-0.3439-0.06830.151-0.00970.0680.17350.0590.230823.636618.721972.4891
59.39911.38721.42955.6380.68436.2181-0.2096-0.14650.20190.5810.15050.6892-0.0348-0.7380.0610.2828-0.00250.15240.33320.09940.209618.960617.751278.5106
64.17051.06020.33538.25852.75665.3551-0.0087-0.6315-0.19970.6422-0.20590.834-0.1257-0.99630.18920.38770.00660.17590.54480.10550.348317.818317.618185.955
75.03-1.7948-1.01624.71042.21434.33330.0947-1.2378-0.25431.5253-0.09680.7707-0.1898-0.50570.05650.66390.06220.25930.80390.11510.408316.853718.790194.893
81.97221.19991.35852.002-0.10162.7909-0.3494-1.21060.66740.4152-0.0090.824-0.576-0.45570.14680.92870.00510.48011.0654-0.1580.68119.738922.971796.7008
94.67920.7962-2.51774.65740.91718.29740.4016-1.0399-0.40890.7361-0.45920.3707-0.4264-1.3059-0.00110.6241-0.07530.04981.19330.18740.455115.2751-1.7592118.005
103.71070.4831-0.5242.373-1.1476.97420.0846-0.8228-0.23750.5513-0.3345-0.1926-0.72610.72490.24070.5388-0.1546-0.12440.56550.1340.332333.70991.666106.1504
119.26063.58120.69715.87530.70125.552-0.2164-0.6023-0.63080.2113-0.3728-1.0115-0.13381.20140.5320.4651-0.0774-0.10740.66270.17470.327842.1232.733292.9716
122.21041.24130.43892.0482-5.27266.1079-0.4038-0.237-0.7346-0.3015-0.3213-1.02960.85940.71310.82560.49830.03330.08790.46690.13610.557441.28792.20786.3101
137.86660.2351-1.04926.0064-0.00116.4209-0.00970.2103-0.4237-0.2915-0.5278-0.96060.64321.05310.45380.31030.11430.00580.52130.16540.37442.90836.914377.8346
142.7699-1.7383-0.45235.1142-1.75321.1125-0.0739-0.1370.65810.7324-0.4034-1.9939-0.26011.58470.40940.46260.004-0.1211.09220.18630.938354.263112.715178.1568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 297 )
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 336 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 213 )
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 242 )
12X-RAY DIFFRACTION12chain 'B' and (resid 243 through 265 )
13X-RAY DIFFRACTION13chain 'B' and (resid 266 through 300 )
14X-RAY DIFFRACTION14chain 'B' and (resid 301 through 338 )

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