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- PDB-7rvf: Segment from the Y169F mutant of the bank vole prion protein 168-... -

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Basic information

Entry
Database: PDB / ID: 7rvf
TitleSegment from the Y169F mutant of the bank vole prion protein 168-176 QFNNQNNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril / human prion
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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: 1 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)1,1241
Polymers1,1241
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 area1360 Å2
Unit cell
Length a, b, c (Å)4.880, 10.560, 29.980
Angle α, β, γ (deg.)93.890, 92.380, 103.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Major prion protein


Mass: 1124.162 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / Mutation: Y169F / Source method: obtained synthetically / Source: (synth.) Myodes glareolus (Bank vole) / References: UniProt: Q8VHV5
#2: Water ChemComp-HOH / 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: 6 / Details: 0.2 M MES, pH 6, 10% MPD

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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: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→10.24 Å / Num. obs: 2938 / % possible obs: 94.8 % / Redundancy: 6.239 % / Biso Wilson estimate: 8.937 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.229 / Rrim(I) all: 0.248 / Χ2: 0.886 / Net I/σ(I): 5.33 / Num. measured all: 18329 / Scaling rejects: 24
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
1-1.035.1540.6362.286342241230.7110.754.9
1.03-1.065.2710.6182.4811862412250.6960.67793.4
1.06-1.095.7860.5252.959721741680.7830.57496.6
1.09-1.125.8280.4173.7312532212150.8350.45697.3
1.12-1.166.10.3734.1814032322300.8840.40599.1
1.16-1.26.3820.3634.5313212092070.870.39599
1.2-1.256.6670.3764.7112401881860.8240.40698.9
1.25-1.35.4880.3594.189001661640.9080.39598.8
1.3-1.355.8320.344.3610091751730.9410.37198.9
1.35-1.426.5510.375.0310351591580.8420.40199.4
1.42-1.56.6310.3715.3911141691680.8850.40399.4
1.5-1.597.4380.2786.9113091771760.9540.29899.4
1.59-1.76.9580.2317.538351211200.9080.2599.2
1.7-1.836.4030.2567.047941261240.9410.2898.4
1.83-2.016.4150.2247.927571211180.9760.24597.5
2.01-2.256.7120.2138.757921201180.9770.23298.3
2.25-2.597.1310.2119.997631081070.8710.22799.1
2.59-3.185.9240.1599.0439169660.990.17595.7
3.18-4.496.8730.18610.7943366630.9570.20195.5
4.49-10.246.4830.14210.2818833290.9880.15187.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 93.89 ° / ∠β: 92.38 ° / ∠γ: 103.29 ° / A: 4.88 Å / B: 10.56 Å / C: 29.98 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→10.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 0.754 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 294 10 %RANDOM
Rwork0.2167 ---
obs0.2202 2644 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 24.1 Å2 / Biso mean: 6.086 Å2 / Biso min: 1.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0 Å2-0.02 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1→10.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 0 2 81
Biso mean---21.24 -
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0080.01280
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0010.01869
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.6621.638107
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg1.3181.64152
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg4.78858
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg49.69927.58
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg11.3571511
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0620.29
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0090.02106
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other00.0230
LS refinement shellResolution: 1.004→1.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 12 -
Rwork0.336 109 -
all-121 -
obs--54.26 %

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