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- PDB-5o0q: Deglycosylated Nogo Receptor with native disulfide structure -

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Basic information

Entry
Database: PDB / ID: 5o0q
TitleDeglycosylated Nogo Receptor with native disulfide structure
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
PHOSPHATE ION / Reticulon-4 receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _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 1.6Oct 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
B: Reticulon-4 receptor
C: Reticulon-4 receptor
D: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,22730
Polymers148,4384
Non-polymers3,79026
Water5,999333
1
A: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28010
Polymers37,1091
Non-polymers1,1719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7425
Polymers37,1091
Non-polymers6324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1478
Polymers37,1091
Non-polymers1,0387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0587
Polymers37,1091
Non-polymers9496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.121, 46.332, 132.232
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 15 molecules ABCD

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


Mass: 37109.387 Da / Num. of mol.: 4
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 (production host): HEK293 / 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.: 11
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

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Non-polymers , 4 types, 348 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M NaH2PO4, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.5→45.94 Å / Num. obs: 53288 / % possible obs: 94.8 % / Redundancy: 2.6 % / CC1/2: 0.992 / Rrim(I) all: 0.181 / Net I/σ(I): 5.8
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1 / CC1/2: 0.472 / Rrim(I) all: 1.091 / % possible all: 96.8

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Processing

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

1ozn


Resolution: 2.5→45.938 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 2772 5.21 %
Rwork0.2111 --
obs0.2137 53220 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 228 333 9680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039594
X-RAY DIFFRACTIONf_angle_d0.56913096
X-RAY DIFFRACTIONf_dihedral_angle_d17.1983550
X-RAY DIFFRACTIONf_chiral_restr0.0421482
X-RAY DIFFRACTIONf_plane_restr0.0041695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.39881260.3322580X-RAY DIFFRACTION97
2.5431-2.58940.35071530.3062576X-RAY DIFFRACTION96
2.5894-2.63920.37541710.30152434X-RAY DIFFRACTION96
2.6392-2.69310.33781400.29262535X-RAY DIFFRACTION96
2.6931-2.75160.3241300.27952548X-RAY DIFFRACTION95
2.7516-2.81560.34751270.27992492X-RAY DIFFRACTION95
2.8156-2.8860.34461430.2982572X-RAY DIFFRACTION96
2.886-2.9640.37181190.30532498X-RAY DIFFRACTION95
2.964-3.05120.34551440.2942549X-RAY DIFFRACTION95
3.0512-3.14970.31031570.25822512X-RAY DIFFRACTION96
3.1497-3.26220.31541340.2362550X-RAY DIFFRACTION95
3.2622-3.39280.27621600.22972506X-RAY DIFFRACTION95
3.3928-3.54720.29421300.22712556X-RAY DIFFRACTION95
3.5472-3.73410.26651430.18232446X-RAY DIFFRACTION93
3.7341-3.96790.23021410.16722325X-RAY DIFFRACTION88
3.9679-4.27410.23291240.15182001X-RAY DIFFRACTION74
4.2741-4.70380.18331500.15012605X-RAY DIFFRACTION98
4.7038-5.38360.17041220.14812693X-RAY DIFFRACTION99
5.3836-6.77920.22921200.17972731X-RAY DIFFRACTION99
6.7792-45.94550.17231380.18612739X-RAY DIFFRACTION96
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)
14.2081-1.03010.04335.5190.72075.71260.09720.47510.1117-0.5609-0.1276-0.0121-0.26490.25680.01020.3064-0.00040.02320.39320.07110.140574.162714.5212107.2854
21.44060.15980.78026.3626-1.20952.7149-0.067-0.0088-0.05-0.10110.1464-0.06680.05610.0999-0.02490.16320.00090.04690.40480.00630.213979.87314.0012118.0793
31.29811.57180.5455.20210.76615.19660.01940.045-0.09310.14670.0843-0.19730.14310.1421-0.08250.16160.0043-0.02240.33860.04010.258377.0019-4.4078130.7592
46.08630.03750.41299.36540.83985.3953-0.33580.1254-0.22340.54190.2245-0.4209-0.19050.29860.04120.2863-0.02810.04810.38670.06030.157772.9292-9.1777141.2446
56.8526-1.8284-2.71045.96594.73174.96080.062-0.19760.05060.39010.136-0.1640.50190.1309-0.12820.3637-0.0335-0.05870.34520.06420.219465.9489-18.4886145.0313
67.8402-1.1107-0.57877.61563.13166.9252-0.13140.2762-0.67740.7108-0.0635-0.40811.3063-0.02110.13690.5129-0.0494-0.03610.40520.16060.377765.0227-26.4148147.5074
76.5470.2341.34719.1594-0.94387.28190.3674-0.68751.06931.1318-0.1758-0.1076-1.2162-0.6119-0.24250.4691-0.06550.08550.4042-0.07230.405121.932540.722591.3139
81.9552-0.2479-0.33935.47053.43035.104-0.18020.1048-0.23980.3529-0.19060.61270.3236-0.4320.32280.2432-0.0250.10550.3992-0.04220.3944112.449326.593283.4958
95.45471.0571-1.814.16020.10078.4110.01780.3532-0.37180.0149-0.28450.63590.4785-0.62040.25530.2971-0.02450.03810.3314-0.1150.4029114.388415.407766.6445
102.5502-1.19993.11196.40313.47577.7624-0.09910.0806-0.2625-0.5813-0.24480.35840.478-0.56060.33760.4412-0.05810.09360.504-0.07440.3629117.2429.286258.1386
112.2326-1.31981.91797.9933-5.00054.7762-0.0120.2884-0.192-0.7814-0.16240.89390.16810.65750.02980.60860.10910.06480.4907-0.13130.3967122.107813.489552.9746
125.2339-0.0353-2.60055.7979-2.89065.563-0.50450.3601-0.9518-0.71140.0648-0.01580.8522-0.54050.39810.55110.03430.07640.4792-0.18060.4869125.69211.136252.8542
133.2081-0.0364-1.50191.4842-1.31695.8614-0.4415-0.4725-0.909-1.39380.15790.43851.88160.01540.07721.14320.1242-0.00880.5042-0.20740.87125.9057-6.991750.4652
143.2662-0.35870.22924.58971.44972.7946-0.1017-0.02290.1204-0.02610.01930.3192-0.0713-0.10210.07750.15890.0138-0.07550.40490.05660.3662105.3508-2.0315118.3897
153.9293-1.82681.13493.261-1.592.04020.01970.188-0.5279-0.17830.0131-0.14890.22240.1243-0.0160.231-0.0102-0.00150.305-0.04820.3365131.3148-22.9234119.9222
162.4579-0.6760.7233.66960.10484.5761-0.2842-0.28340.20070.13970.1535-0.6141-0.44990.74920.090.3331-0.0997-0.11940.52440.04480.442788.190428.652979.6511
172.37670.0686-0.34294.30581.79285.8338-0.1749-0.04330.08450.20440.0189-0.3236-0.31340.26260.12310.2824-0.0228-0.06340.43650.0530.250677.167918.126884.8081
183.6122-0.53592.38145.17010.52682.07650.1052-0.2051-0.1430.4358-0.0843-0.04410.02080.07750.03570.2883-0.02550.01930.45790.02790.202364.57229.744581.4279
193.67771.00130.85823.37440.05064.41030.0458-0.4162-0.05060.4694-0.00580.15820.1419-0.13820.01920.2336-0.00180.03830.4017-0.00830.224956.04893.605978.6338
202.40413.042-6.20777.1394-2.21648.9845-0.29430.3380.804-0.96780.32481.88770.7921-0.91430.02160.40730.0172-0.16110.54950.02720.266850.72857.892873.9271
215.4057-1.89242.18457.6988-0.9384.6891-0.2503-0.1142-0.38090.12770.16150.38710.422-0.3660.07930.3205-0.0480.04560.4222-0.05980.278149.754-7.733969.864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 256 )
5X-RAY DIFFRACTION5chain 'A' and (resid 257 through 290 )
6X-RAY DIFFRACTION6chain 'A' and (resid 291 through 336 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 242 )
11X-RAY DIFFRACTION11chain 'B' and (resid 243 through 256 )
12X-RAY DIFFRACTION12chain 'B' and (resid 257 through 290 )
13X-RAY DIFFRACTION13chain 'B' and (resid 291 through 336 )
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 116 )
15X-RAY DIFFRACTION15chain 'C' and (resid 117 through 336 )
16X-RAY DIFFRACTION16chain 'D' and (resid 25 through 83 )
17X-RAY DIFFRACTION17chain 'D' and (resid 84 through 156 )
18X-RAY DIFFRACTION18chain 'D' and (resid 157 through 213 )
19X-RAY DIFFRACTION19chain 'D' and (resid 214 through 242 )
20X-RAY DIFFRACTION20chain 'D' and (resid 243 through 256 )
21X-RAY DIFFRACTION21chain 'D' and (resid 257 through 336 )

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