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- PDB-3nvh: MIHFGND segment 137-143 from mouse prion -

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Basic information

Entry
Database: PDB / ID: 3nvh
TitleMIHFGND segment 137-143 from mouse prion
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / activation of protein kinase activity / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / negative regulation of long-term synaptic potentiation / response to cadmium ion / side of membrane / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / nuclear membrane / response to oxidative stress / protease binding / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / membrane raft / copper ion binding / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
trifluoroacetic acid / Major prion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsApostol, M.I. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Biochemistry / Year: 2011
Title: Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.
Authors: Apostol, M.I. / Wiltzius, J.J. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9482
Polymers8341
Non-polymers1141
Water543
1
A: Major prion protein
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)9,48020
Polymers8,33910
Non-polymers1,14010
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation3_574-x,y+5/2,-z-1/21
crystal symmetry operation3_564-x,y+3/2,-z-1/21
crystal symmetry operation3_554-x,y+1/2,-z-1/21
crystal symmetry operation3_544-x,y-1/2,-z-1/21
crystal symmetry operation3_534-x,y-3/2,-z-1/21
Unit cell
Length a, b, c (Å)30.280, 4.873, 31.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 833.932 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: MIHFGND peptide (residues 137-143) from mouse prion
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925
#2: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.38 Å3/Da / Density % sol: 10.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES ph 7.0, 10% PEG 1200, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466 Å
DetectorType: MAR CCD 165 / Detector: CCD / Date: Dec 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.61→90 Å / Num. obs: 714 / % possible obs: 97.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.206 / Χ2: 1.038 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.61-1.712.70.28551.05288.7
1.71-1.7830.216620.92793.9
1.78-1.8630.265571.17595
1.86-1.963.10.16640.97294.1
1.96-2.085.60.229701.07598.6
2.08-2.247.70.258781.09998.7
2.24-2.466.60.219861.015100
2.46-2.82100.303621.027100
2.82-3.5510.30.205751.025100
3.55-908.10.1571051.02100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å21.7 Å
Translation2.5 Å21.7 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→21.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.1692 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8962 / SU B: 1.641 / SU ML: 0.057 / SU R Cruickshank DPI: 0.1375 / SU Rfree: 0.1171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 72 10.3 %RANDOM
Rwork0.1659 ---
obs0.169 696 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.48 Å2 / Biso mean: 12.4124 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.61→21.7 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms58 0 7 3 68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0241
X-RAY DIFFRACTIONr_angle_refined_deg1.2972.00397
X-RAY DIFFRACTIONr_angle_other_deg0.6093101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.995254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4681512
X-RAY DIFFRACTIONr_chiral_restr0.0880.29
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0214
X-RAY DIFFRACTIONr_mcbond_it0.8271.542
X-RAY DIFFRACTIONr_mcbond_other0.2041.515
X-RAY DIFFRACTIONr_mcangle_it1.469266
X-RAY DIFFRACTIONr_scbond_it1.535331
X-RAY DIFFRACTIONr_scangle_it2.1144.531
LS refinement shellResolution: 1.61→1.797 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.299 23 -
Rwork0.232 120 -
all-143 -
obs--79.44 %

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