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- PDB-5o0p: Deglycosylated Nogo Receptor with native disulfide structure 6 -

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Basic information

Entry
Database: PDB / ID: 5o0p
TitleDeglycosylated Nogo Receptor with native disulfide structure 6
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 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_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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
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

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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)75,93713
Polymers74,2192
Non-polymers1,71911
Water4,558253
1
A: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8655
Polymers37,1091
Non-polymers7564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0728
Polymers37,1091
Non-polymers9637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.208, 46.891, 121.795
Angle α, β, γ (deg.)90.00, 123.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-404-

NA

21B-611-

HOH

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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
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 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M citric acid, 0.05 M Bis-Tris propane pH 5.0, 16 % (w/v) PEG3350
PH range: 5

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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→44.08 Å / Num. obs: 48789 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rrim(I) all: 0.109 / Net I/σ(I): 8.5
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1 / CC1/2: 0.593 / Rrim(I) all: 1.329 / % possible all: 99.6

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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→43.525 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 2341 4.8 %
Rwork0.1842 --
obs0.1856 48741 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 109 253 4952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064839
X-RAY DIFFRACTIONf_angle_d1.2116601
X-RAY DIFFRACTIONf_dihedral_angle_d18.8941802
X-RAY DIFFRACTIONf_chiral_restr0.045750
X-RAY DIFFRACTIONf_plane_restr0.005857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.33991340.32382730X-RAY DIFFRACTION99
2.0408-2.08520.33441610.30682628X-RAY DIFFRACTION99
2.0852-2.13370.35411470.28892717X-RAY DIFFRACTION98
2.1337-2.18710.27841530.27222655X-RAY DIFFRACTION99
2.1871-2.24620.33141360.24932724X-RAY DIFFRACTION99
2.2462-2.31230.25631130.23952715X-RAY DIFFRACTION99
2.3123-2.38690.2541410.22672719X-RAY DIFFRACTION99
2.3869-2.47220.27051180.22142789X-RAY DIFFRACTION100
2.4722-2.57120.24011280.20522696X-RAY DIFFRACTION99
2.5712-2.68820.24061310.19192729X-RAY DIFFRACTION99
2.6882-2.82990.22041400.19182730X-RAY DIFFRACTION100
2.8299-3.00720.24371360.20182744X-RAY DIFFRACTION100
3.0072-3.23930.21691270.19462737X-RAY DIFFRACTION99
3.2393-3.56510.22181410.17472736X-RAY DIFFRACTION99
3.5651-4.08070.16761530.14152737X-RAY DIFFRACTION99
4.0807-5.140.14991360.13412750X-RAY DIFFRACTION98
5.14-43.53570.17441460.15852864X-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)
18.37250.86813.10082.16212.22517.50710.15140.11190.1198-0.2725-0.30150.1327-0.2231-0.6170.25730.32970.0439-0.02770.37040.00970.203270.196147.614724.3315
25.0146-1.93030.92084.7958-0.71793.6170.12480.3504-0.0426-0.4535-0.1541-0.21790.31120.07040.02940.3074-0.00030.01210.26120.01810.149582.169139.36425.8427
34.22490.4831.03736.9504-1.62495.5612-0.03280.3498-0.0389-0.5462-0.1219-0.30060.43690.46260.12970.27770.05630.03720.24760.02040.180491.403827.756737.2598
45.53581.06250.21028.5643-0.91995.8146-0.1218-0.0228-0.05170.0658-0.0449-0.70720.27990.69430.17310.27190.0686-0.00290.33870.06140.173695.794521.961449.9415
53.94421.41860.67558.61181.02256.66420.2085-0.2452-0.44920.0332-0.1349-0.41320.40920.2341-0.040.28070.05010.01850.28160.05450.206393.110212.582657.3768
67.1443-0.520.19326.7265-0.19445.23760.0921-0.0026-1.06680.1460.046-1.03220.80090.3273-0.13530.56590.049-0.08580.43260.05840.532394.42534.064859.2557
75.0538-2.19920.43646.425-1.39075.10290.18390.28050.6756-0.2512-0.1662-0.4437-0.11130.8124-0.02310.1805-0.04030.04850.44060.00760.3478142.156436.3649-6.5601
83.65470.4171-0.65623.0783-0.87424.69290.0071-0.14940.14790.10310.0316-0.23360.10740.5992-0.05230.15270.0159-0.0280.3386-0.04970.2312137.467625.89574.8593
94.56161.6141-1.19637.17730.94294.11320.0662-0.26790.01890.3460.0011-0.01260.060.1401-0.08640.16880.0392-0.04130.2858-0.01510.2218125.89617.416610.9301
104.98192.7804-0.17197.3811.81175.83040.1415-0.597-0.09050.557-0.06080.04340.19750.1547-0.0950.15960.0243-0.03410.34570.00660.2295117.642311.168514.5802
112.10480.45381.88359.39220.11458.54620.1113-0.25490.00810.5523-0.24140.7436-0.3189-0.913-0.08350.23050.00860.04430.4401-0.01040.4353110.565915.297114.5822
126.3184-0.0387-0.25177.27881.76293.20180.0764-0.3285-0.03440.252-0.03270.09040.2908-0.2703-0.06750.1911-0.0212-0.04840.26990.02270.2086107.89853.115311.762
135.3178-0.6222-0.50246.7655-1.82348.0645-0.0298-0.8021-0.69921.23850.0878-0.42770.60250.3592-0.00290.5357-0.0502-0.11760.52790.05810.4239106.5438-5.645914.2545
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 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 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 83 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 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 338 )

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