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- PDB-6axz: Segment from bank vole prion protein 168-176 QYNNQNNFV -

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Basic information

Entry
Database: PDB / ID: 6axz
TitleSegment from bank vole prion protein 168-176 QYNNQNNFV
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / polar clasp / amyloid fibril / prion
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / 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 speciesMyodes glareolus (Bank vole)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / cryo EM / Resolution: 0.75 Å
Model detailspolar clasp, MicroED, Glutamine ladder, Asparagine ladder
AuthorsGlynn, C. / Rodriguez, J.A. / Boyer, D.R. / Gallagher-Jones, M.
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp.
Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / ...Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / Gustavo F Helguera / James E Evans / Michael R Sawaya / Duilio Cascio / David S Eisenberg / Tamir Gonen / Jose A Rodriguez /
Abstract: The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution ...The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)1,1401
Polymers1,1401
Non-polymers00
Water362
1
A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein

A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)11,40210
Polymers11,40210
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_765x+2,y+1,z1
crystal symmetry operation1_865x+3,y+1,z1
crystal symmetry operation1_965x+4,y+1,z1
Unit cell
Length a, b, c (Å)4.940, 10.340, 31.150
Angle α, β, γ (deg.)94.210, 92.380, 102.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Major prion protein


Mass: 1140.162 Da / Num. of mol.: 1 / Fragment: UNP residues 168-176 / Source method: obtained synthetically / Source: (synth.) Myodes glareolus (Bank vole) / References: UniProt: Q8VHV5
#2: Water ChemComp-HOH / water / 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: bank vole prion 168-176 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.0046 MDa / Experimental value: YES
Source (natural)Organism: Myodes glareolus (Bank vole)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
Crystal growTemperature: 298 K / Method: batch mode / pH: 6 / Details: 10% MPD, 0.1 M MES, pH 6.0

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.025 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffractionCamera length: 950 mm
EM diffraction shellResolution: 0.75→0.77 Å / Fourier space coverage: 96.2 % / Multiplicity: 4.4 / Num. of structure factors: 532 / Phase residual: 0.01 °
EM diffraction statsFourier space coverage: 97.1 % / High resolution: 0.75 Å / Num. of intensities measured: 43252 / Num. of structure factors: 7474 / Phase error: 0.01 ° / Phase residual: 0.01 ° / Phase error rejection criteria: 0 / Rmerge: 23.2 / Rsym: 23.2
DiffractionMean temperature: 100 K
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 0.75→10.338 Å / Num. obs: 7474 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 5.787 % / Biso Wilson estimate: 4.17 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.232 / Rrim(I) all: 0.25 / Χ2: 0.872 / Net I/σ(I): 4.57 / Num. measured all: 43252 / Scaling rejects: 7
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
0.75-0.774.4340.6381.7723595535320.2090.72996.2
0.77-0.794.9750.5812.3327715825570.3830.65595.7
0.79-0.815.2250.5432.5727385495240.4830.60695.4
0.81-0.845.0460.5142.5725185204990.510.57996
0.84-0.875.1340.4792.8424444894760.6110.53597.3
0.87-0.95.4120.4263.2625224874660.7750.47195.7
0.9-0.935.6850.3773.8326324794630.8330.41496.7
0.93-0.976.1630.3634.4228354754600.8660.39396.8
0.97-1.016.2450.3124.9227044434330.9170.33697.7
1.01-1.065.8190.3364.922813983920.8910.36698.5
1.06-1.126.1140.2855.4923603883860.9460.30999.5
1.12-1.196.8260.2746.4525943853800.9390.29498.7
1.19-1.276.7790.266.5325493783760.9490.2899.5
1.27-1.376.0030.2576.417472992910.930.2897.3
1.37-1.56.630.2437.1220223113050.950.26198.1
1.5-1.686.8760.2167.818912872750.960.23195.8
1.68-1.946.0540.2017.5112412112050.9670.21897.2
1.94-2.376.7730.2098.2214902222200.9650.22599.1
2.37-3.356.570.1688.49921551510.9820.1897.4
3.35-10.3386.7710.2058.656288830.9680.21894.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
EM softwareName: Coot / Category: model refinement
EM 3D crystal entity∠α: 94.21 ° / ∠β: 92.38 ° / ∠γ: 102.2 ° / A: 4.94 Å / B: 10.34 Å / C: 31.15 Å / Space group name: P1 / Space group num: 1
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 6.068 / Protocol: AB INITIO MODEL / Space: RECIPROCAL / Target criteria: maximum likelihood
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.75→10.338 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 36.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 673 9.01 %0
Rwork0.2422 6800 --
obs0.2426 7473 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 17.71 Å2 / Biso mean: 6.0686 Å2 / Biso min: 1.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01482
ELECTRON CRYSTALLOGRAPHYf_angle_d1.014111
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.10410
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00517
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d18.83829
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.7495-0.80740.39071340.36831358149295
0.8074-0.88860.36621300.34421313144397
0.8886-1.01710.28591370.28591383152097
1.0171-1.2810.2621370.24361391152899
1.281-10.33870.18511350.18751355149097

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