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

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Basic information

Entry
Database: PDB / ID: 6btk
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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
DepositionDec 6, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)1,1401
Polymers1,1401
Non-polymers00
Water724
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)4.874, 10.107, 30.415
Angle α, β, γ (deg.)93.360, 91.150, 101.660
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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.28 Å3/Da / Density % sol: 4.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6, 10% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2016
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.1→100 Å / Num. obs: 1867 / % possible obs: 80.8 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.1 / Rrim(I) all: 0.142 / Χ2: 1.81 / Net I/σ(I): 5.7 / Num. measured all: 3070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.1-1.141.20.4031100.5320.4030.570.50946.2
1.14-1.181.50.3771420.5590.3640.5240.93160.2
1.18-1.241.50.4131830.4560.4050.5791.24274.4
1.24-1.31.60.3111920.6250.310.4391.11891.4
1.3-1.391.60.242060.8280.2340.3361.14793.6
1.39-1.491.60.1952040.8570.1910.2731.0785.7
1.49-1.641.80.1471860.9290.1460.2071.66676.2
1.64-1.881.80.1051980.9760.1040.1481.68797.1
1.88-2.371.80.1052450.9680.1040.1472.77796.5
2.37-1001.80.0792010.9820.0790.1123.42790.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.1 Å30.42 Å
Translation1.1 Å30.42 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→30.35 Å / WRfactor Rfree: 0.1712 / WRfactor Rwork: 0.1381 / FOM work R set: 0.8355 / SU B: 1.702 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0515 / SU Rfree: 0.0445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 179 9.6 %RANDOM
Rwork0.139 ---
obs0.1409 1688 80.75 %-
Displacement parametersBiso max: 39.73 Å2 / Biso mean: 11.888 Å2 / Biso min: 8.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0.15 Å2-0.23 Å2
2---0.52 Å2-0.15 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.1→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 0 4 85
Biso mean---23.1 -
Num. residues----9
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 6 -
Rwork0.287 68 -
all-74 -
obs--40.88 %

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