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- PDB-5o0r: Deglycosylated Nogo Receptor with native disulfide structure -

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Basic information

Entry
Database: PDB / ID: 5o0r
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
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 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Jul 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 1.3Jan 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 1.4Oct 23, 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)75,61512
Polymers74,2192
Non-polymers1,39710
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Small angle X-ray scattering suggests self-association that could represent dimerization on the cell surface
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-6 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.728, 111.654, 114.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37109.387 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 / Cell (production host): HEK293 / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): GntI-/- / 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.: 5
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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.8 M NaH2PO4/K2HPO4 pH 5.0

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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: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.73 Å / Num. obs: 21264 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rsym value: 0.213 / Net I/σ(I): 3.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.663 / Rsym value: 0.811 / % possible all: 99.8

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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→43.105 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 983 4.64 %
Rwork0.2522 --
obs0.2546 21186 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4505 0 85 29 4619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024714
X-RAY DIFFRACTIONf_angle_d0.5476427
X-RAY DIFFRACTIONf_dihedral_angle_d12.22829
X-RAY DIFFRACTIONf_chiral_restr0.043728
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.63190.37411270.32192886X-RAY DIFFRACTION100
2.6319-2.79680.41531330.32852865X-RAY DIFFRACTION99
2.7968-3.01270.34941500.31942849X-RAY DIFFRACTION99
3.0127-3.31570.39921520.31542845X-RAY DIFFRACTION98
3.3157-3.79530.26031180.23962832X-RAY DIFFRACTION96
3.7953-4.78070.24981420.19322881X-RAY DIFFRACTION97
4.7807-43.11170.2651610.22623045X-RAY DIFFRACTION99
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)
14.4272.7130.41644.08230.20441.8115-0.50950.8385-1.345-0.3548-0.031-0.25310.5532-0.10850.37520.6823-0.51880.12380.5005-0.2820.97434.225459.182449.3532
24.6786-0.051-1.47844.11162.24345.13480.04411.0514-0.564-0.0993-0.18920.47590.3173-0.25810.09120.3832-0.0474-0.03150.4736-0.09550.328513.049960.392842.7441
36.5242-4.09220.03946.0271-0.77493.6130.03230.5216-0.3102-0.3023-0.14760.48050.0397-0.25990.06560.4962-0.1442-0.04320.3593-0.04250.243422.074169.279438.7362
48.2425-4.2113-0.94547.3292.052.4328-0.01990.778-0.177-0.1419-0.59340.124-0.0680.17810.40110.4566-0.08620.01070.3313-0.02710.241926.747679.626238.3242
57.3689-2.3632-1.49874.87790.88578.090.08220.44650.1672-0.0516-0.1072-0.05080.3864-0.5295-0.13890.3093-0.0471-0.05310.18530.03810.202230.212884.882442.9393
64.81481.53111.41012.466-0.65994.96170.27380.02510.1902-0.3754-0.0349-0.01730.1495-0.0108-0.24460.36150.03990.02990.156-0.01190.212536.933792.887847.5345
76.0493-2.636-0.14874.72611.49493.32710.61080-0.0054-0.0886-0.56290.05740.18570.1311-0.05480.3808-0.0216-0.01980.19150.01920.301443.087298.750953.9967
83.4026-1.87111.1545.5128-1.70177.7437-0.5070.18430.62470.0317-0.1535-0.798-0.8390.57380.49840.4699-0.1096-0.14810.39830.02730.523652.227999.257654.5634
96.32013.11550.63178.17020.37211.9647-0.180.3708-0.80460.0720.3414-1.1350.72790.4045-0.12680.9280.15290.10170.4090.05690.559257.454457.541111.6124
107.41852.3544-0.19236.8308-1.95564.45920.1157-0.4885-0.5004-0.3459-0.4406-0.64090.30670.10440.25620.34860.1286-0.00480.25630.02060.249850.876865.289517.6133
117.17060.8085-1.34484.00470.03012.70780.2711-0.2592-0.05910.3857-0.2801-0.0858-0.37630.1457-0.02540.54260.1214-0.0010.30120.07420.330743.401274.713220.9637
126.42121.8807-2.07882.8963-0.82094.33530.4387-0.1979-0.77240.8586-0.21310.174-0.3385-0.3702-0.16870.45540.18040.01070.47870.11770.397837.835380.503517.6031
139.54791.8261.52566.65750.93047.4704-0.41010.12760.64120.96960.45250.3056-0.313-0.47520.00210.57610.180.03670.26420.06620.226839.983882.494813.6838
146.2759-0.41830.5867.4228-1.75186.3385-0.0946-0.17880.2210.78650.51260.0743-0.5876-0.6954-0.38420.54260.0484-0.04930.31540.06540.275633.398391.640412.0519
154.996-1.88390.88957.0312-0.6038.5722-0.33830.13320.30030.47670.77642.01870.169-0.4844-0.32930.35430.03080.10650.34920.18060.597221.912798.0045.3659
163.1919-2.1676-0.85634.985-0.04133.0945-0.07780.33820.6021-0.7597-0.33311.6077-0.1654-0.6702-0.00640.56540.1874-0.37150.3259-0.00641.240818.771997.4991-0.0461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 290 )
8X-RAY DIFFRACTION8chain 'A' and (resid 291 through 336 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 57 )
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 156 )
12X-RAY DIFFRACTION12chain 'B' and (resid 157 through 175 )
13X-RAY DIFFRACTION13chain 'B' and (resid 176 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 256 )
15X-RAY DIFFRACTION15chain 'B' and (resid 257 through 277 )
16X-RAY DIFFRACTION16chain 'B' and (resid 278 through 335 )

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