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- PDB-8iia: Crystal structure of the oligomeric state of the extracellular do... -

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Basic information

Entry
Database: PDB / ID: 8iia
TitleCrystal structure of the oligomeric state of the extracellular domain of human myelin protein zero(MPZ/P0)
ComponentsMyelin protein P0
KeywordsCELL ADHESION / membrane adhesion / oligomeric state
Function / homology
Function and homology information


cell aggregation / : / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination / myelin sheath / chemical synaptic transmission / synapse / structural molecule activity / plasma membrane
Similarity search - Function
Myelin protein P0, C-terminal / Myelin P0 protein, conserved site / : / Myelin-PO cytoplasmic C-term p65 binding region / Myelin P0 protein signature. / Myelin P0 protein-related / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Myelin protein P0, C-terminal / Myelin P0 protein, conserved site / : / Myelin-PO cytoplasmic C-term p65 binding region / Myelin P0 protein signature. / Myelin P0 protein-related / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSakakura, M. / Tanabe, M. / Mio, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06515 Japan
Japan Society for the Promotion of Science (JSPS)18K06601 Japan
Japan Science and TechnologyJP18071859 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama1210001j001 Japan
CitationJournal: Structure / Year: 2023
Title: Structural bases for the Charcot-Marie-Tooth disease induced by single amino acid substitutions of myelin protein zero.
Authors: Sakakura, M. / Tanabe, M. / Mori, M. / Takahashi, H. / Mio, K.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1592
Polymers14,0671
Non-polymers921
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.579, 88.579, 88.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Myelin protein P0 / Myelin peripheral protein / MPP / Myelin protein zero / MPZ/P0


Mass: 14066.645 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPZ / Production host: Escherichia coli B (bacteria) / References: UniProt: P25189
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 300 mM magnesium-formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→44.49 Å / Num. obs: 10861 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 49.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.028 / Net I/av σ(I): 13.9 / Net I/σ(I): 13.9
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 27.4 % / Rmerge(I) obs: 3.297 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 815 / CC1/2: 0.815 / Rpim(I) all: 0.634 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NEU

1neu


Resolution: 2.09→36.27 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.1569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 501 4.62 %
Rwork0.2167 10343 -
obs0.2174 10844 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.75 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 6 51 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461029
X-RAY DIFFRACTIONf_angle_d0.69591402
X-RAY DIFFRACTIONf_chiral_restr0.0524146
X-RAY DIFFRACTIONf_plane_restr0.0061179
X-RAY DIFFRACTIONf_dihedral_angle_d8.5501136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.30.33881370.28962503X-RAY DIFFRACTION99.44
2.3-2.630.35811240.27842547X-RAY DIFFRACTION99.89
2.63-3.310.27541100.24322590X-RAY DIFFRACTION99.96
3.31-36.270.19031300.18932703X-RAY DIFFRACTION99.93

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