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- PDB-7rvh: Q172E mutant of the bank vole prion protein 168-176 QYNNENNFV -

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Basic information

Entry
Database: PDB / ID: 7rvh
TitleQ172E mutant of the bank vole prion protein 168-176 QYNNENNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
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
Biological speciesMyodes glareolus (Bank vole)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / Resolution: 0.9 Å
AuthorsGlynn, C. / Rodriguez, J.A. / Hernandez, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI143368 United States
CitationJournal: To be published
Title: Structural and Biophysical Consequences of Sequence Variation in the B2a2 Loop of Mammalian Prions
Authors: Glynn, C. / Hernandez, E. / Gallagher-Jones, M. / Miao, J. / Rodriguez, J.A.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)1,1411
Polymers1,1411
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1380 Å2
Unit cell
Length a, b, c (Å)4.870, 10.060, 30.660
Angle α, β, γ (deg.)94.850, 90.260, 99.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Major prion protein


Mass: 1141.147 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / Mutation: Q172E / Source method: obtained synthetically / Source: (synth.) Myodes glareolus (Bank vole) / References: UniProt: Q8VHV5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Major prion protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Myodes glareolus (Bank vole)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M lithium sulfate, 2.5 M sodium chloride, 0.1 M sodium acetate, pH 4.5

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Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1
EM diffractionCamera length: 1 mm
DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: OTHER / Wavelength: 0.0251 Å
DetectorType: TVIPS TEMCAM-F416 / Detector: CMOS / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 0.9→7.98 Å / Num. obs: 3437 / % possible obs: 81 % / Redundancy: 5.383 % / Biso Wilson estimate: 6.859 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.214 / Χ2: 0.824 / Net I/σ(I): 5.21 / Num. measured all: 18502 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.9-0.934.8580.4752.5616034013300.7830.52982.3
0.93-0.975.0680.3923.320174873980.8120.43581.7
0.97-1.015.0530.3893.2715313713030.8940.43281.7
1.01-1.075.1030.3094.1418374543600.9390.34279.3
1.07-1.135.3280.2824.9717053843200.9230.30983.3
1.13-1.225.50.2825.4920684603760.910.3181.7
1.22-1.345.4160.2725.6317173943170.9340.29980.5
1.34-1.545.8570.2466.6321324513640.9370.26780.7
1.54-1.935.7990.2037.5718503973190.9720.2280.4
1.93-7.985.8340.1518.6120424433500.9860.16379

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 94.85 ° / ∠β: 90.26 ° / ∠γ: 99.99 ° / A: 4.87 Å / B: 10.06 Å / C: 30.66 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 0.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→7.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 0.445 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 310 9 %RANDOM
Rwork0.2207 ---
obs0.222 3126 81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 34.91 Å2 / Biso mean: 4.586 Å2 / Biso min: 0.84 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 0.9→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 0 2 83
Biso mean---12.64 -
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0090.01182
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0010.01867
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.3061.67111
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.5471.625148
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg4.1658
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg51.54127.58
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg14.9141511
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.1040.29
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.010.02113
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other00.0227
LS refinement shellResolution: 0.9→0.923 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 23 -
Rwork0.302 232 -
all-255 -
obs--80.7 %

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