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- PDB-1py9: The crystal structure of an autoantigen in multiple sclerosis -

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Basic information

Entry
Database: PDB / ID: 1py9
TitleThe crystal structure of an autoantigen in multiple sclerosis
ComponentsMyelin-oligodendrocyte glycoprotein
KeywordsIMMUNE SYSTEM / myelin sheath / multiple sclerosis / receptor / immunoglobulin / anti-parallel dimer
Function / homology
Function and homology information


regulation of cytokine production / myelin sheath / T cell receptor signaling pathway / cell adhesion / signaling receptor binding / external side of plasma membrane / cell surface
Similarity search - Function
Myelin-oligodendrocyte glycoprotein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Myelin-oligodendrocyte glycoprotein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myelin-oligodendrocyte glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsClements, C.S. / Reid, H.H. / Beddoe, T. / Tynan, F.E. / Perugini, M.A. / Johns, T.G. / Bernard, C.C. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The crystal structure of myelin oligodendrocyte glycoprotein, a key autoantigen in multiple sclerosis
Authors: Clements, C.S. / Reid, H.H. / Beddoe, T. / Tynan, F.E. / Perugini, M.A. / Johns, T.G. / Bernard, C.C. / Rossjohn, J.
History
DepositionJul 8, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 11, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin-oligodendrocyte glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4703
Polymers13,2781
Non-polymers1922
Water3,873215
1
A: Myelin-oligodendrocyte glycoprotein
hetero molecules

A: Myelin-oligodendrocyte glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9406
Polymers26,5562
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)65.720, 65.720, 67.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1183-

HOH

Detailsmonomer in the asymmtric unit. However a crystallographic, head-to-tail dimer is present

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Components

#1: Protein Myelin-oligodendrocyte glycoprotein


Mass: 13277.826 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MOG / Production host: Escherichia coli (E. coli) / References: UniProt: Q61885
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.25 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
1300 mMimidazole in sodium phosphate/Tris1droppH8.0
250 mM1dropNaCl
35 mMTris1droppH8.0
41.3 mg/mlprotein1drop
514-18 %PEG40001reservoir
60.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 13229 / Num. obs: 13229 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.069 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.246 / Rsym value: 0.018 / % possible all: 100
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 33022 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B7.2

Resolution: 1.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1312 -random
Rwork0.201 ---
obs0.201 13229 99 %-
all-13229 --
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 10 215 1159
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.005
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.35
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg26.3
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.7

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