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- EMDB-38081: Conventional Reconstruction of the MC-45 de novo processed riboso... -

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Basic information

Entry
Database: EMDB / ID: EMD-38081
TitleConventional Reconstruction of the MC-45 de novo processed ribosome 50S
Map data
Sample
  • Complex: E. coli 70S ribosome, from EMPIAR-10509
Keywordsribosome 50S / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 3.16 Å
AuthorsZhang XZ / Zhu DJ / Cao WL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 and 32150010 China
CitationJournal: Sci Adv / Year: 2024
Title: Correction of preferred orientation-induced distortion in cryo-electron microscopy maps.
Authors: Dongjie Zhu / Weili Cao / Junxi Li / Chunling Wu / Duanfang Cao / Xinzheng Zhang /
Abstract: Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been ...Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building.
History
DepositionNov 20, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38081.png

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Map

FileDownload / File: emd_38081.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 384 pix.
= 363.517 Å		0.95 Å/pix.
x 384 pix.
= 363.517 Å		0.95 Å/pix.
x 384 pix.
= 363.517 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94666 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-1.134259 - 1.88799
Average (Standard dev.)0.008452887 (±0.10250312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 363.51743 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38081_msk_1.map
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Half map: #2

Fileemd_38081_half_map_1.map
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Half map: #1

Fileemd_38081_half_map_2.map
Projections & Slices
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Sample components

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Entire : E. coli 70S ribosome, from EMPIAR-10509

EntireName: E. coli 70S ribosome, from EMPIAR-10509
Components
  • Complex: E. coli 70S ribosome, from EMPIAR-10509

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Supramolecule #1: E. coli 70S ribosome, from EMPIAR-10509

SupramoleculeName: E. coli 70S ribosome, from EMPIAR-10509 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Details: We used EMPIAR-10509. This repository was not recorded by us.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22586

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 38800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)

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