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- EMDB-19667: Cryo-electron tomogram of keyhole limpet hemocyanin -

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-19667
TitleCryo-electron tomogram of keyhole limpet hemocyanin
Map data
  • Complex: Keyhole limpet hemocyanin (KLH)
KeywordsKeyhole limpet hemocyanin / KLH / METAL BINDING PROTEIN
Biological speciesMegathura crenulata (invertebrata)
Methodelectron tomography / cryo EM
AuthorsComet M / Dijkman PM / Boer Iwema R / Franke T / Masiulis S / Schampers R / Raschdorf O / Grollios F / Pryor Jr EE / Drulyte I
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows.
Authors: Maxime Comet / Patricia M Dijkman / Reint Boer Iwema / Tilman Franke / Simonas Masiulis / Ruud Schampers / Oliver Raschdorf / Fanis Grollios / Edward E Pryor / Ieva Drulyte /
Abstract: Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that ...Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.
DepositionFeb 17, 2024-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

Structure visualization

Supplemental images

Downloads & links


FileDownload / File: emd_19667.map.gz / Format: CCP4 / Size: 544 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
6 Å/pix.
x 272 pix.
= 1632. Å
6 Å/pix.
x 1024 pix.
= 6144. Å
6 Å/pix.
x 1024 pix.
= 6144. Å


Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6 Å
Minimum - Maximum-32768.0 - 32767.0
Average (Standard dev.)5041.769500000000335 (±3713.12480000000005)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA: 6144.0 Å / B: 6144.0 Å / C: 1632.0 Å
α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : Keyhole limpet hemocyanin (KLH)

EntireName: Keyhole limpet hemocyanin (KLH)
  • Complex: Keyhole limpet hemocyanin (KLH)

Supramolecule #1: Keyhole limpet hemocyanin (KLH)

SupramoleculeName: Keyhole limpet hemocyanin (KLH) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Megathura crenulata (invertebrata)

Experimental details

Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 41 / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT)
Details: Reconstruction was obtained using Tomo Live on-the-fly reconstruction pipeline
Number images used: 41

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