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- PDB-7rvd: Segment from the mouse/cow prion protein 168-176 QYSNQNNFV -

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Basic information

Entry
Database: PDB / ID: 7rvd
TitleSegment from the mouse/cow prion protein 168-176 QYSNQNNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril / mouse / cow
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / 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 / ATP-dependent protein binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / 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 / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / nucleobase-containing compound metabolic process / 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 / response to amyloid-beta / negative regulation of type II interferon production / cuprous ion binding / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / 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 / regulation of protein localization / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynaptic density / 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 / metal ion binding / identical protein binding / membrane / 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 speciesMus musculus (house mouse)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / Resolution: 1.003 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. / Rodriguez, J.A. / Hernandez, E.
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)1,1131
Polymers1,1131
Non-polymers00
Water00
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, 10.170, 31.290
Angle α, β, γ (deg.)94.650, 90.730, 101.150
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 1113.137 Da / Num. of mol.: 1 / Fragment: UNP residues 167-175 / Source method: obtained synthetically / Details: also Bos taurus / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925

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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: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.5 M zinc acetate, 15% ethanol, 0.2 M MES, pH 6

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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: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→10.391 Å / Num. obs: 2977 / % possible obs: 93.9 % / Redundancy: 2.996 % / Biso Wilson estimate: 4.54 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.197 / Χ2: 0.952 / Net I/σ(I): 3.99 / Num. measured all: 8918 / 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
1-1.032.4330.5141.335232272150.7420.6594.7
1.03-1.052.540.4781.514802071890.8060.59891.3
1.05-1.082.5120.3172.155402322150.9060.39392.7
1.08-1.122.7680.2852.686202352240.9050.34795.3
1.12-1.153.0250.3342.985992101980.860.39994.3
1.15-1.23.1330.2963.096582222100.9350.35594.6
1.2-1.242.7980.2712.935121911830.9280.32995.8
1.24-1.293.0060.2743.364871681620.9390.32596.4
1.29-1.352.9180.2373.54641661590.9390.28495.8
1.35-1.413.1170.2463.835331811710.9220.29494.5
1.41-1.493.40.2224.755441711600.9450.26193.6
1.49-1.583.4910.2015.165691701630.9690.23395.9
1.58-1.693.4440.176.124651471350.9490.19891.8
1.69-1.832.970.1635.542971081000.9640.19992.6
1.83-23.1880.1536.434081371280.9870.18293.4
2-2.243.2290.1217.33391121050.9860.14593.8
2.24-2.583.7140.1268.26364108980.9720.14690.7
2.58-3.163.030.097.7120374670.9940.10690.5
3.16-4.473.2770.1298.8521370650.9880.15192.9
4.47-10.3913.3330.1717.8110034300.9750.19488.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 94.65 ° / ∠β: 90.73 ° / ∠γ: 101.15 ° / A: 4.87 Å / B: 10.17 Å / C: 31.29 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 1.003 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.003→10.391 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 265 9.03 %
Rwork0.2011 2670 -
obs0.2056 2935 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.87 Å2 / Biso mean: 8.4907 Å2 / Biso min: 1.19 Å2
Refinement stepCycle: final / Resolution: 1.003→10.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 0 0 79
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00880
ELECTRON CRYSTALLOGRAPHYf_angle_d0.92108
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.09610
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00516
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d15.24928
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.0035-1.26390.25661290.1994130091
1.2639-100.24711360.2019137097

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