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- PDB-7rvl: Segment from the Y169F mutant of the human prion protein 168-176 ... -

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Basic information

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


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 / NCAM1 interactions / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...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 / NCAM1 interactions / 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 protein processing / negative regulation of dendritic spine maintenance / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / long-term memory / response to cadmium ion / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / 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 / 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 / postsynapse / regulation of cell cycle / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
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)1,0981
Polymers1,0981
Non-polymers00
Water181
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 area1350 Å2
Unit cell
Length a, b, c (Å)4.900, 10.380, 30.260
Angle α, β, γ (deg.)90.910, 90.820, 102.250
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 1098.122 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / Mutation: Y169F / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: Homo sapiens (human)
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 sodium acetate, pH 4.5, 1 M sodium chloride, 0.1 M lithium sulfate

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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: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→10.14 Å / Num. obs: 2737 / % possible obs: 87.1 % / Redundancy: 5.357 % / Biso Wilson estimate: 4.34 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.197 / Χ2: 0.881 / Net I/σ(I): 5.99 / Num. measured all: 14661 / Scaling rejects: 20
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
1-1.035.0060.3633.668162341630.940.469.7
1.03-1.054.8850.333.658942231830.9530.3682.1
1.05-1.085.3930.2954.029061941680.9640.3286.6
1.08-1.125.270.2794.5110542302000.9450.30487
1.12-1.155.4740.2595.3510402211900.9340.28286
1.15-1.26.1590.2555.9111212051820.9570.27688.8
1.2-1.245.780.2285.6610752081860.9730.24789.4
1.24-1.294.7730.2764.727161701500.8760.31288.2
1.29-1.355.1720.2345.717501631450.9510.25989
1.35-1.415.1310.2675.717851691530.8520.29990.5
1.41-1.495.280.2486.078291711570.9120.28191.8
1.49-1.585.9490.2277.399281691560.930.2592.3
1.58-1.695.8240.1848.057631441310.9350.20491
1.69-1.834.4770.1766.554791171070.9490.20291.5
1.83-25.0790.1767.955791251140.9850.19691.2
2-2.245.5890.178.625981181070.9650.18990.7
2.24-2.585.8820.1569.56001141020.9580.17489.5
2.58-3.164.2960.1337.523265540.9570.15683.1
3.16-4.475.60.13110.5433667600.9910.14389.6
4.47-10.145.5170.09710.1816036290.9860.10780.6

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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: 90.91 ° / ∠β: 90.82 ° / ∠γ: 102.25 ° / A: 4.9 Å / B: 10.38 Å / C: 30.26 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→10.14 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 247 9.04 %
Rwork0.1897 2486 -
obs0.1915 2733 87.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 24.2 Å2 / Biso mean: 8.0612 Å2 / Biso min: 0.93 Å2
Refinement stepCycle: final / Resolution: 1→10.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77 0 0 1 78
Biso mean---24.2 -
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 (%)
1-1.260.21271200.19551204132484
1.26-10.140.20961270.1871282140990

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