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- PDB-7rve: Segment from the S170N mutant of the human prion protein 168-176 ... -

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Basic information

Entry
Database: PDB / ID: 7rve
TitleSegment from the S170N mutant of the human prion protein 168-176 EYNNQNNFV
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: 0.85 Å
AuthorsGlynn, C. / Rodriguez, J.A. / Hernandez, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 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)1,1411
Polymers1,1411
Non-polymers00
Water362
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 area1390 Å2
Unit cell
Length a, b, c (Å)4.930, 10.140, 31.560
Angle α, β, γ (deg.)94.130, 90.590, 102.740
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: 1141.147 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / Mutation: S170N / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 0.85→9.86 Å / Num. obs: 4694 / % possible obs: 89.8 % / Redundancy: 3.547 % / Biso Wilson estimate: 5.33 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.211 / Χ2: 0.883 / Net I/σ(I): 3.81 / Num. measured all: 16649 / 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
0.85-0.872.4350.5051.223923731610.6170.63143.2
0.87-0.92.7640.4831.547493542710.740.58776.6
0.9-0.923.0210.4291.8510153913360.7670.51385.9
0.92-0.953.4550.3972.1711783603410.8770.45894.7
0.95-0.983.6890.3162.7412913623500.9260.36396.7
0.98-1.023.6160.3312.612153443360.910.38497.7
1.02-1.053.4950.3322.899752882790.9170.38396.9
1.05-1.13.5220.3173.3510323042930.9040.36596.4
1.1-1.153.9020.2844.2411983173070.910.32296.8
1.15-1.23.5860.254.2910042892800.9410.28996.9
1.2-1.274.0770.2494.6111092822720.9540.28396.5
1.27-1.343.4260.2464.17162222090.9490.2994.1
1.34-1.443.7430.2534.939022512410.9630.28796
1.44-1.553.6790.2195.288242332240.9350.2596.1
1.55-1.74.10.1956.568242152010.9620.21893.5
1.7-1.93.270.1675.654841591480.9710.19693.1
1.9-2.23.7820.1756.476241761650.9670.20393.8
2.2-2.694.090.1497.265441421330.980.16793.7
2.69-3.83.6990.1247.41344102930.9820.1491.2
3.8-9.864.2410.1398.4322962540.9720.15687.1

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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: 94.13 ° / ∠β: 90.59 ° / ∠γ: 102.74 ° / A: 4.93 Å / B: 10.14 Å / C: 31.56 Å / Space group name: P212121 / Space group num: 19
3D reconstructionResolution: 0.85 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.85→9.86 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 38.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 422 8.99 %
Rwork0.2128 4270 -
obs0.2177 4692 89.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.53 Å2 / Biso mean: 23.5867 Å2 / Biso min: 0.93 Å2
Refinement stepCycle: final / Resolution: 0.85→9.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 0 2 83
Biso mean---22.27 -
Num. residues----9
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.85-0.970.33131240.27431249137378
0.97-1.230.28691510.25341543169497
1.23-9.860.2461470.18421478162594

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