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- EMDB-7287: MicroED structure of carbamazepine at 0.85 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-7287
TitleMicroED structure of carbamazepine at 0.85 A resolution
Map data2Fo-Fc MicroED map of Carbamazepine (CBZ)
Sample
  • Complex: Carbamazepine
Biological speciesunidentified (others)
Methodelectron crystallography / cryo EM / Resolution: 0.85 Å
AuthorsGallagher-Jones M / Glynn C / Boyer DR / Martynowycz MW / Hernandez E / Miao J / Zee CT / NoviKova IV / Goldschmidt L / McFarlane HT ...Gallagher-Jones M / Glynn C / Boyer DR / Martynowycz MW / Hernandez E / Miao J / Zee CT / NoviKova IV / Goldschmidt L / McFarlane HT / Helguera GF / Evans JE / Sawaya MR / Cascio D / Eisenberg D / Gonen T / Rodriguez JA
Funding support United States, 4 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Science Foundation (NSF, United States)DMR 1548924 United States
Department of Energy (DOE, United States)Project FWP #66382 United States
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 7, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7287.png

Downloads & links

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Map

FileDownload / File: emd_7287.map.gz / Format: CCP4 / Size: 68.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2Fo-Fc MicroED map of Carbamazepine (CBZ)
Voxel sizeX=Y=Z: 0.281 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 0.6
Minimum - Maximum-1.417186 - 2.4729836
Average (Standard dev.)2.1282513e-10 (±0.34598488)
SymmetrySpace group: 14
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions285611
Spacing284056
CellA: 7.8679996 Å / B: 11.24 Å / C: 15.735999 Å
α: 90.0 ° / β: 93.2 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.2810.2810.281
M x/y/z284056
origin x/y/z0.0000.0000.000
length x/y/z7.86811.24015.736
α/β/γ90.00093.20090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS562811
D min/max/mean-1.4172.4730.000

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Supplemental data

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Additional map: Fo MicroED map of Carbamazepine (CBZ)

Fileemd_7287_additional_1.map
AnnotationFo MicroED map of Carbamazepine (CBZ)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Fo-Fc MicroED map of Carbamazepine (CBZ)

Fileemd_7287_additional_2.map
AnnotationFo-Fc MicroED map of Carbamazepine (CBZ)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Carbamazepine

EntireName: Carbamazepine
Components
  • Complex: Carbamazepine

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Supramolecule #1: Carbamazepine

SupramoleculeName: Carbamazepine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Carbamazepine is a small molecule inhibitor of sodium channels used primarily in the treatment of epilepsy.
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 234 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.33 / Component - Concentration: 1.0 mg/mL / Component - Formula: C2H5OH / Component - Name: Ethanol / Details: Pure ethanol
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: NITROGEN / Chamber humidity: 30 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Plunge-frozen after 10 seconds of blotting..
DetailsPowder was dissolved in ethanol at 1 mg/mL and applied to EM grids.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 70.0 K / Max: 100.0 K
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 120 / Number diffraction images: 120 / Average exposure time: 5.0 sec. / Average electron dose: 0.01 e/Å2
Details: MicroED was collected under continuous rotation at a rate of 0.1 degrees/second with each frame corresponding to 5 seconds of exposure with a total range of tilts between -30 and +30 degrees.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 730 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN / Tilt angle: -30.0, 30.0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 0.85 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystal parametersUnit cell - A: 7.5 Å / Unit cell - B: 11.0 Å / Unit cell - C: 13.70 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 93.2 ° / Space group: P21/n
Crystallography statisticsNumber intensities measured: 2598 / Number structure factors: 956 / Fourier space coverage: 49.4 / R sym: 0.105 / R merge: 0.086 / Overall phase error: 30 / Overall phase residual: 30 / Phase error rejection criteria: 0 / High resolution: 0.85 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.85 Å / Shell - Low resolution: 7.5 Å / Shell - Number structure factors: 956 / Shell - Phase residual: 20 / Shell - Fourier space coverage: 49.4 / Shell - Multiplicity: 2.7

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 10 / Target criteria: CC

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