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- PDB-7rvk: Segment from Y169G mutant of the human prion protein 169-175 GSNQNNF -

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Basic information

Entry
Database: PDB / ID: 7rvk
TitleSegment from Y169G mutant of the human prion protein 169-175 GSNQNNF
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 / 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 / tubulin binding / 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 / 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 / regulation of cell cycle / postsynapse / 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 / cytoplasm / 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
ACETATE ION / Major prion protein
Similarity search - Component
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9043
Polymers7801
Non-polymers1242
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-15 kcal/mol
Surface area1160 Å2
Unit cell
Length a, b, c (Å)4.860, 14.110, 18.410
Angle α, β, γ (deg.)90.000, 93.710, 101.210
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: 779.756 Da / Num. of mol.: 1 / Fragment: UNP residues 169-175 / Mutation: Y169G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 6
Details: 10% w/v PEG8000, 0.1 M MES, pH 6, 0.2 M sodium acetate

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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: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→13.84 Å / Num. obs: 2076 / % possible obs: 80.3 % / Redundancy: 6.217 % / Biso Wilson estimate: 3.58 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.238 / Rrim(I) all: 0.257 / Χ2: 0.775 / Net I/σ(I): 5.05 / Num. measured all: 12907 / Scaling rejects: 2
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
1-1.034.260.432.255241901230.8620.48564.7
1.03-1.055.6860.4072.917961741400.8760.44680.5
1.05-1.086.4050.3823.599481791480.8440.41382.7
1.08-1.126.3090.3643.818771731390.8780.39480.3
1.12-1.166.9070.3424.5711121941610.8980.36683
1.16-1.26.7160.3024.569941751480.9150.32784.6
1.2-1.246.8670.3324.918241511200.7940.35979.5
1.24-1.295.5910.3024.527101531270.9470.33483
1.29-1.355.5890.2994.745981341070.9070.32579.9
1.35-1.416.2710.3224.867401431180.90.35182.5
1.41-1.496.4580.2975.76911301070.9320.32282.3
1.49-1.587.4210.3056.398981441210.9280.32684
1.58-1.696.4780.2496.71583115900.8940.2778.3
1.69-1.835.3860.2456.02447103830.9180.26980.6
1.83-26.0620.2076.95485100800.9450.22580
2-2.246.190.2117.5148997790.9390.22981.4
2.24-2.587.2250.1998.0351387710.9670.21381.6
2.58-3.165.4550.1846.9224057440.9780.19977.2
3.16-4.476.0960.2028.1731761520.9790.21785.2
4.47-13.846.7220.1597.7212126180.9760.17169.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.0refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
EM 3D crystal entity∠α: 90 ° / ∠β: 93.71 ° / ∠γ: 101.21 ° / A: 4.86 Å / B: 14.11 Å / C: 18.41 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→13.84 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.04 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 208 10.02 %RANDOM
Rwork0.1984 ---
obs0.2024 2075 80.3 %-
Displacement parametersBiso max: 26.76 Å2 / Biso mean: 5.74 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.0165 Å20.1179 Å20.2173 Å2
2--0.2353 Å2-0.1016 Å2
3----0.2188 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: final / Resolution: 1→13.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55 0 8 6 69
Biso mean--8.71 14.52 -
Num. residues----7
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
ELECTRON CRYSTALLOGRAPHYt_dihedral_angle_d19SINUSOIDAL2
ELECTRON CRYSTALLOGRAPHYt_trig_c_planes5HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_gen_planes18HARMONIC5
ELECTRON CRYSTALLOGRAPHYt_it103HARMONIC20
ELECTRON CRYSTALLOGRAPHYt_nbd1SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_improper_torsion
ELECTRON CRYSTALLOGRAPHYt_pseud_angle
ELECTRON CRYSTALLOGRAPHYt_chiral_improper_torsion6SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_sum_occupancies
ELECTRON CRYSTALLOGRAPHYt_utility_distance
ELECTRON CRYSTALLOGRAPHYt_utility_angle
ELECTRON CRYSTALLOGRAPHYt_utility_torsion
ELECTRON CRYSTALLOGRAPHYt_ideal_dist_contact93SEMIHARMONIC4
ELECTRON CRYSTALLOGRAPHYt_bond_d103HARMONIC20.01
ELECTRON CRYSTALLOGRAPHYt_angle_deg175HARMONIC20.94
ELECTRON CRYSTALLOGRAPHYt_omega_torsion3.14
ELECTRON CRYSTALLOGRAPHYt_other_torsion24.6
LS refinement shellResolution: 1→1.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2223 55 10 %
Rwork0.2067 495 -
all0.2084 550 -
obs--80.3 %

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