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- PDB-7rvc: Segment from the human prion protein 168-176 EYSNQNNFV -

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Basic information

Entry
Database: PDB / ID: 7rvc
TitleSegment from the human prion protein 168-176 EYSNQNNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / amyloid / prion / fibril
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 / positive regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / 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 / positive regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / 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 / extrinsic component of membrane / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / long-term memory / 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 / intracellular signal transduction / postsynaptic density / 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 / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / 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: 1.002 Å
AuthorsGlynn, C. / Rodriguez, J.A. / Hernandez, E.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI143368
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)1,1141
Polymers1,1141
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 area1370 Å2
Unit cell
Length a, b, c (Å)10.020, 4.890, 31.330
Angle α, β, γ (deg.)90.990, 91.420, 102.180
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: 1114.122 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / 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 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% ethanol, 0.1 M sodium acetate, pH 4.5, 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: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→10.437 Å / Num. obs: 3031 / % possible obs: 97.6 % / Redundancy: 5.203 % / Biso Wilson estimate: 4.42 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.207 / Χ2: 0.855 / Net I/σ(I): 5.56 / Num. measured all: 15771 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1-1.034.1020.4322.111670.840.49277
1.03-1.064.8560.4652.651940.7870.5295.6
1.06-1.095.1170.3373.332310.9090.375100
1.09-1.125.2970.2884.232190.9340.318100
1.12-1.165.5720.3014.642010.8990.33100
1.16-1.25.8290.3044.662160.9190.33499.5
1.2-1.245.390.2834.782000.9210.313100
1.24-1.295.1130.274.711680.9420.30199.4
1.29-1.354.920.2375.011630.9630.265100
1.35-1.425.3140.2445.511720.9450.271100
1.42-1.495.5090.2116.371650.9660.233100
1.49-1.585.710.2027.121620.9680.22298.8
1.58-1.695.290.1767.631550.9610.195100
1.69-1.834.8480.2037.561050.9540.22699.1
1.83-24.870.1657.981310.970.18599.2
2-2.245.4130.169.231090.9680.177100
2.24-2.595.4060.1389.531060.9720.15397.2
2.59-3.174.4720.1539.07720.9670.17197.3
3.17-4.485.0310.189.96650.990.19598.5
4.48-105.2330.10310.16300.990.11485.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 90.99 ° / ∠β: 91.42 ° / ∠γ: 102.18 ° / A: 10.02 Å / B: 4.89 Å / C: 31.33 Å / Space group name: P1 / Space group num: 1
3D reconstructionResolution: 1.002 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.002→10.437 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 302 9.98 %
Rwork0.1627 2724 -
obs0.1632 3026 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.55 Å2 / Biso mean: 9.1631 Å2 / Biso min: 1.04 Å2
Refinement stepCycle: final / Resolution: 1.002→10.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79 0 0 1 80
Biso mean---20.04 -
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01780
ELECTRON CRYSTALLOGRAPHYf_angle_d1.607108
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0910
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00816
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d14.07628
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.002-1.26210.18811480.1737134696
1.2621-100.15861540.1578137899

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