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- PDB-7rvi: Segment from naked mole rat (elk T174S) prion protein 168-176 QYN... -

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Basic information

Entry
Database: PDB / ID: 7rvi
TitleSegment from naked mole rat (elk T174S) prion protein 168-176 QYNNQNSFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril / naked mole rat
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / 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
CACODYLATE ION / Major prion protein
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / Resolution: 1.05 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2733
Polymers1,1131
Non-polymers1602
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area1590 Å2
Unit cell
Length a, b, c (Å)62.760, 4.850, 21.520
Angle α, β, γ (deg.)90.000, 109.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Major prion protein


Mass: 1113.137 Da / Num. of mol.: 1 / Fragment: UNP residues 158-166 / Source method: obtained synthetically / Source: (synth.) Heterocephalus glaber (naked mole-rat) / References: UniProt: G5B4V6
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: Heterocephalus glaber (naked mole-rat)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 5% isopropanol, 0.1 M zinc acetate

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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: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1.05→10.76 Å / Num. obs: 2612 / % possible obs: 79.9 % / Redundancy: 8.391 % / Biso Wilson estimate: 2.75 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.287 / Rrim(I) all: 0.305 / Χ2: 0.748 / Net I/σ(I): 5 / Num. measured all: 21917 / Scaling rejects: 15
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
1.05-1.088.5610.5892.4716012241870.9130.62383.5
1.08-1.118.7620.515316212201850.9050.54484.1
1.11-1.148.7880.4633.4516612271890.9090.48883.3
1.14-1.179.3470.4423.6818322411960.890.46681.3
1.17-1.219.7430.4334.0518222251870.910.45683.1
1.21-1.267.5830.4093.9610921801440.8880.43680
1.26-1.37.550.344.2111401861510.9690.36281.2
1.3-1.367.7340.4024.0211061761430.8790.42781.2
1.36-1.427.9080.3264.6511231791420.9290.34679.3
1.42-1.499.0130.3135.4913881871540.9580.33182.4
1.49-1.579.2850.3365.6713371791440.970.35580.4
1.57-1.6690.2556.8511971671330.9720.26979.6
1.66-1.787.1430.2916.057501331050.910.31178.9
1.78-1.927.2940.2946.267951351090.9410.31380.7
1.92-2.17.2750.2996.817931381090.9240.31879
2.1-2.358.7480.2178.469711351110.9810.2382.2
2.35-2.717.2780.2227.86575107790.950.23873.8
2.71-3.326.5250.2757.8439887610.9390.29570.1
3.32-4.79.2770.19610.360394650.9940.20769.1
4.7-10.766.2220.1527.9911248180.9910.16137.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 90 ° / ∠β: 109.14 ° / ∠γ: 90 ° / A: 62.76 Å / B: 4.85 Å / C: 21.52 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 1.05 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→10.76 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 262 10.03 %
Rwork0.2222 2350 -
obs0.2271 2612 80.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 12.92 Å2 / Biso mean: 3.9399 Å2 / Biso min: 0.75 Å2
Refinement stepCycle: final / Resolution: 1.05→10.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 6 3 88
Biso mean--9.46 9.01 -
Num. residues----9
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.320.26381290.21191161129082
1.32-10.760.26551330.2281189132278

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