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- PDB-1ozn: 1.5A Crystal Structure of the Nogo Receptor Ligand Binding Domain... -

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Basic information

Entry
Database: PDB / ID: 1ozn
Title1.5A Crystal Structure of the Nogo Receptor Ligand Binding Domain Reveals a Convergent Recognition Scaffold Mediating Inhibition of Myelination
ComponentsReticulon 4 receptor
KeywordsSIGNALING PROTEIN / Nogo Receptor / MAD / Myelination Inhibition / Omgp / MAG / nogo-66 / p75 / Signal Transduction / Neuronal Regeneration / Ligand Binding
Function / homology
Function and homology information


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 / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction ...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 / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / dendritic shaft / positive regulation of GTPase activity / negative regulation of neuron projection development / presynapse / signaling receptor activity / heparin binding / 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 / extracellular exosome / plasma membrane
Similarity search - Function
Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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 ...Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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
ACETIC ACID / Reticulon-4 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.52 Å
AuthorsHe, X. / Bazan, J.F. / Park, J.B. / McDermott, G. / He, Z. / Garcia, K.C.
CitationJournal: Neuron / Year: 2003
Title: Structure of the Nogo Receptor Ectodomain. A Recognition module implicated in Myelin Inhibition.
Authors: He, X.L. / Bazan, J.F. / McDermott, G. / Park, J.B. / Wang, K. / Tessier-Lavigne, M. / He, Z. / Garcia, K.C.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulon 4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1296
Polymers31,6131
Non-polymers1,5155
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.206, 33.915, 60.221
Angle α, β, γ (deg.)85.02, 75.91, 67.96
Int Tables number1
Space group name H-MP1
DetailsThe Nogo Receptor ligand binding domain binds myelin inhibtors such as Nogo, Omgp and MAG

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Components

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


Mass: 31613.375 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTN4R OR NOGOR / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9BZR6
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-3-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.87 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG4000, sodium chloride, sodium acetate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
235 %PEG40001reservoir
30.25 M1reservoirNaCl
40.1 Msodium acetate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0064, 1.0096, 0.9950
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00641
21.00961
30.9951
ReflectionResolution: 1.52→50 Å / Num. all: 33484 / Num. obs: 33484 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 7.4 / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 96.4 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.52→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.198 1634 RANDOM
Rwork0.167 --
all0.168 32883 -
obs0.168 32883 -
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-3.31 Å2-1.55 Å2
2--1.51 Å21.9 Å2
3----2.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 101 354 2674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shellResolution: 1.52→1.62 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection
Rfree0.276 262
Rwork0.214 -
obs-4761
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
LS refinement shell
*PLUS
Lowest resolution: 1.56 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226

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