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- PDB-7rvg: Segment from rabbit/pig prion protein 168-176 QYSNQNSFV -

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Basic information

Entry
Database: PDB / ID: 7rvg
TitleSegment from rabbit/pig prion protein 168-176 QYSNQNSFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril / rabbit / pig
Function / homology
Function and homology information


aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade ...aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / negative regulation of type II interferon production / cuprous ion binding / positive regulation of protein targeting to membrane / side of membrane / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / cellular response to copper ion / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein homooligomerization / protein destabilization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / learning or memory / intracellular signal transduction / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / identical protein binding / plasma membrane / cytosol
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 speciesOryctolagus cuniculus (rabbit)
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)1,0861
Polymers1,0861
Non-polymers00
Water724
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 area1450 Å2
Unit cell
Length a, b, c (Å)23.570, 4.860, 27.700
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1086.112 Da / Num. of mol.: 1 / Fragment: UNP residues 167-175 / Source method: obtained synthetically / Details: also Sus scrofa / Source: (synth.) Oryctolagus cuniculus (rabbit) / References: UniProt: Q95211
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: Oryctolagus cuniculus (rabbit)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.05 M CHES, pH 9, 0.2 M lithium sulfate, 1.3 M sodium/potassium tartrate

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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→7.18 Å / Num. obs: 2680 / % possible obs: 74.9 % / Redundancy: 7.375 % / Biso Wilson estimate: 4.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.204 / Rrim(I) all: 0.22 / Χ2: 0.947 / Net I/σ(I): 5.72 / Num. measured all: 19765 / Scaling rejects: 11
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
1-1.036.6280.6982.4511932511800.6990.76771.7
1.03-1.057.4380.5023.1613762361850.8730.54378.4
1.05-1.087.3870.4913.5813742411860.8420.53577.2
1.08-1.127.7010.3534.3614172361840.9650.38378
1.12-1.158.0340.3064.8214302341780.9360.3376.1
1.15-1.28.1580.4374.2815502391900.8070.47179.5
1.2-1.247.7270.3584.8912442101610.9110.38676.7
1.24-1.297.0340.3035.2510341991470.9460.3373.9
1.29-1.357.3660.3265.0910681971450.9470.35173.6
1.35-1.417.610.3974.910731911410.9060.42973.8
1.41-1.497.7730.3465.510961851410.8140.37476.2
1.49-1.588.2030.2247.7312141901480.9680.24177.9
1.58-1.696.8650.1936.818651641260.9850.2176.8
1.69-1.836.2910.2376.486921511100.9340.25972.8
1.83-26.6760.1748.557011391050.9850.18975.5
2-2.247.6150.179.858301411090.9840.18477.3
2.24-2.587.5060.13410.65668127890.9930.14570.1
2.58-3.165.4680.1269.133994620.9890.14166
3.16-4.476.6760.1113.4345493680.9970.11873.1
4.47-7.185.880.10711.3114758250.9990.11343.1

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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: 111.21 ° / ∠γ: 90 ° / A: 23.57 Å / B: 4.86 Å / C: 27.7 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→7.18 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 263 9.89 %
Rwork0.2182 2395 -
obs0.2184 2658 74.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 17.36 Å2 / Biso mean: 5.5722 Å2 / Biso min: 2.44 Å2
Refinement stepCycle: final / Resolution: 1→7.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77 0 0 4 81
Biso mean---11.45 -
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 (%)
1-1.260.27731300.25861188131876
1.26-7.180.19111330.1981207134074

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