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- PDB-5o0k: Deglycosylated Nogo Receptor with native disulfide structure -

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Basic information

Entry
Database: PDB / ID: 5o0k
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


Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / corpus callosum development / negative chemotaxis ...Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / corpus callosum development / negative chemotaxis / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / dendritic shaft / axon guidance / positive regulation of GTPase activity / presynapse / negative regulation of neuron projection development / signaling receptor activity / heparin binding / growth cone / perikaryon / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / neuronal cell body / glutamatergic synapse / protein-containing complex binding / 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: 2.3 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 1.3Jul 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 1.4Jan 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

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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)74,10118
Polymers72,0222
Non-polymers2,07816
Water4,234235
1
A: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0229
Polymers36,0111
Non-polymers1,0118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0799
Polymers36,0111
Non-polymers1,0678
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.624, 46.586, 120.670
Angle α, β, γ (deg.)90.00, 123.45, 90.00
Int Tables number5
Space group name H-MC121

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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): cystatin secretion signal and C-terminal His6-tag
Cell (production host): HEK293 / Cell line (production host): HEK293 / 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 / N-Acetylglucosamine


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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.15 % / Description: needle
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.05 M citric acid pH 5.0, 15 % (w/v) polyethylene glycol (PEG) 6000

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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: 2.3→43.783 Å / Num. obs: 31309 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.936 / Rsym value: 0.131 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.546 / Rsym value: 0.724 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZN

1ozn


Resolution: 2.3→43.783 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.2338 1517 4.86 %
Rwork0.1787 --
obs0.1813 31191 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 129 235 4916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024833
X-RAY DIFFRACTIONf_angle_d0.656567
X-RAY DIFFRACTIONf_dihedral_angle_d11.411760
X-RAY DIFFRACTIONf_chiral_restr0.025744
X-RAY DIFFRACTIONf_plane_restr0.003854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37430.34511370.26542646X-RAY DIFFRACTION98
2.3743-2.45910.32511460.25162702X-RAY DIFFRACTION98
2.4591-2.55760.28151430.23452662X-RAY DIFFRACTION99
2.5576-2.6740.30391420.22452657X-RAY DIFFRACTION98
2.674-2.81490.29241280.2032712X-RAY DIFFRACTION98
2.8149-2.99120.27671370.2112667X-RAY DIFFRACTION99
2.9912-3.22210.2531450.20232722X-RAY DIFFRACTION99
3.2221-3.54630.23021350.18032703X-RAY DIFFRACTION98
3.5463-4.05910.18821330.14792680X-RAY DIFFRACTION98
4.0591-5.11280.16311280.13162753X-RAY DIFFRACTION98
5.1128-43.79050.21031430.15442770X-RAY DIFFRACTION97
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)
14.56161.43330.87554.85460.95633.51270.1898-0.29120.54870.3512-0.08640.2975-0.0398-0.5807-0.0720.16420.02760.04890.3848-0.01450.3358-22.263833.551556.8201
22.8668-1.4957-0.41972.14010.73541.42030.05710.1098-0.0127-0.05930.0072-0.01650.0178-0.1076-0.06060.1636-0.0619-0.03990.22770.03920.1997-8.013116.926240.9013
35.45410.5643-1.39437.7847-0.66765.1464-0.02660.4553-0.2939-0.28570.04170.04670.56430.19910.00010.20810.0292-0.0580.2507-0.02740.25612.2641-2.638938.2916
45.7577-1.00910.846.2181-3.24998.26540.0797-0.17440.14710.1334-0.2029-0.2672-0.14390.6390.09230.2308-0.0329-0.02090.2857-0.01450.191848.89444.842626.1465
53.82660.1186-0.03215.69360.10652.60320.1347-0.1706-0.05070.2808-0.13570.07570.23530.1496-0.02280.2735-0.0036-0.02340.2439-0.03410.116639.358437.892625.5682
63.0385-0.5415-0.63144.7344-0.88033.63470.0609-0.17180.16340.2675-0.13280.1840.3236-0.4920.04470.3368-0.0939-0.05860.3179-0.07030.228231.162932.768322.5034
75.2990.2946-0.61194.8666-1.49094.51750.1566-0.3275-0.35420.5734-0.22630.24850.4413-0.41570.06020.3984-0.074-0.00560.2644-0.10940.183129.449127.685120.2071
85.5164-1.0243-0.05775.0036-1.44232.4866-0.0451-0.18310.16570.3080.0659-0.20910.3326-0.1135-0.02430.3591-0.0430.01190.2538-0.08240.153328.499224.914.8801
94.5209-0.6270.01469.2135-0.58493.317-0.0797-0.0297-0.02370.1985-0.10220.20920.3374-0.29410.16460.3408-0.04990.01170.2671-0.0650.152326.748323.89459.2404
106.0139-1.6749-0.13587.0301-0.74884.0422-0.1639-0.05760.00540.06780.05840.41470.1507-0.54480.08010.2525-0.0721-0.01640.2747-0.05660.148723.408119.39220.8568
114.5283-1.79330.83486.2535-0.79865.31420.1470.0358-0.68680.201-0.10550.470.4238-0.3054-0.06540.3219-0.07740.020.3051-0.05230.256325.55026.8082-7.5792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 57 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 156 )
8X-RAY DIFFRACTION8chain 'B' and (resid 157 through 175 )
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 256 )
11X-RAY DIFFRACTION11chain 'B' and (resid 257 through 336 )

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