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- EMDB-11603: Human heavy-chain apoferritin refined from tilt series data using M -

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Basic information

Entry
Database: EMDB / ID: EMD-11603
TitleHuman heavy-chain apoferritin refined from tilt series data using M
Map data
Sample
  • Complex: Heavy-chain apoferritin
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 2.3 Å
AuthorsTegunov D / Xue L / Dienemann C / Cramer P / Mahamid J
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP1935 Germany
European Research Council (ERC)693023 Germany
Volkswagen Foundation Germany
European Research Council (ERC)760067 Germany
CitationJournal: Nat Methods / Year: 2021
Title: Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.
Authors: Dimitry Tegunov / Liang Xue / Christian Dienemann / Patrick Cramer / Julia Mahamid /
Abstract: Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and ...Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
History
DepositionAug 7, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000918
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.000918
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11603.png

Downloads & links

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Map

FileDownload / File: emd_11603.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.42 Å/pix.
x 340 pix.
= 141.1 Å		0.42 Å/pix.
x 340 pix.
= 141.1 Å		0.42 Å/pix.
x 340 pix.
= 141.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.415 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000918 / Movie #1: 0.000918
Minimum - Maximum-0.002197574 - 0.0041498253
Average (Standard dev.)3.378256e-05 (±0.0004467794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 141.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4150.4150.415
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z141.100141.100141.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0020.0040.000

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Supplemental data

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Mask #1

Fileemd_11603_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11603_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11603_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Heavy-chain apoferritin

EntireName: Heavy-chain apoferritin
Components
  • Complex: Heavy-chain apoferritin

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Supramolecule #1: Heavy-chain apoferritin

SupramoleculeName: Heavy-chain apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 500 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration3.8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 18991
ExtractionNumber tomograms: 37 / Number images used: 18991 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Software - details: initial assignment / Details: On-the-fly correction in M
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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