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- EMDB-7501: 1.01 A MicroED structure of GSNQNNF at 0.17 e- / A^2 -

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Basic information

Entry
Database: EMDB / ID: EMD-7501
Title1.01 A MicroED structure of GSNQNNF at 0.17 e- / A^2
Map dataMicroED density map
Sample
  • Complex: Synthetic proto-filament
    • Protein or peptide: GSNQNNF
  • Ligand: ACETATE ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsAmyloid fibril / prion / zinc binding / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodelectron crystallography / cryo EM / Resolution: 1.01 Å
AuthorsHattne J / Shi D
CitationJournal: Structure / Year: 2018
Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.
Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen /
Abstract: Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
History
DepositionMar 2, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseMay 16, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44538
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.44538
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7501.png

Downloads & links

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Map

FileDownload / File: emd_7501.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMicroED density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.32 Å/pix.
x 85 pix.
= 26.73 Å		0.31 Å/pix.
x 60 pix.
= 25.925 Å		0.34 Å/pix.
x 83 pix.
= 20.331 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.305 Å / Y: 0.32205 Å / Z: 0.33885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44538 / Movie #1: 0.44538
Minimum - Maximum-1.3812275 - 4.6054873
Average (Standard dev.)-0.0030163813 (±0.2969195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-36-723
Dimensions608385
Spacing858360
CellA: 25.925001 Å / B: 26.73015 Å / C: 20.331 Å
α: 83.603 ° / β: 84.977 ° / γ: 83.307 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.3050.322048192771080.33885
M x/y/z858360
origin x/y/z0.0000.0000.000
length x/y/z25.92526.73020.331
α/β/γ83.60384.97783.307
start NX/NY/NZ-3623-7
NX/NY/NZ608583
MAP C/R/S312
start NC/NR/NS-7-3623
NC/NR/NS836085
D min/max/mean-1.3814.605-0.003

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Supplemental data

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Sample components

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Entire : Synthetic proto-filament

EntireName: Synthetic proto-filament
Components
  • Complex: Synthetic proto-filament
    • Protein or peptide: GSNQNNF
  • Ligand: ACETATE ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Synthetic proto-filament

SupramoleculeName: Synthetic proto-filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Molecular weightTheoretical: 899.141 Da

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Macromolecule #1: GSNQNNF

MacromoleculeName: GSNQNNF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 779.756 Da
SequenceString:
GSNQNNF

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Macromolecule #2: ACETATE ION

MacromoleculeName: ACETATE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACT
Molecular weightTheoretical: 59.044 Da
Chemical component information

ChemComp-ACT:
ACETATE ION

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
0.1 MC6H13NO4SMES
10.0 %C6H14O2MPD
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 1012 / Number diffraction images: 1012 / Average exposure time: 2.1 sec. / Average electron dose: 0.00357 e/Å2
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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.01 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 14826 / Number structure factors: 1941 / Fourier space coverage: 78 / R sym: 0.224 / R merge: 0.224 / Overall phase error: 28.16 / Overall phase residual: 28.16 / Phase error rejection criteria: 0 / High resolution: 1.01 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.01 Å / Shell - Low resolution: 1.04 Å / Shell - Number structure factors: 125 / Shell - Phase residual: 41.15 / Shell - Fourier space coverage: 74.85 / Shell - Multiplicity: 6.1

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Atomic model buiding 1

DetailsElectron scattering factors
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 1.79
Output model

PDB-6cli:
1.01 A MicroED structure of GSNQNNF at 0.17 e- / A^2

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