Numerical Methods of Cryo Electron Tomography

Group leader
Daniel Castaño

Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)

Research goal

We develop software and algorithmic methods for cryo-electron tomography (cryoET). Our inhouse package Dynamo covers all stages of this computational pipeline: alignment of tilt series, reconstruction of tomograms, particle extraction and subtomogram averaging and classification. Using constitutive exocytosis in yeast cells as experimental example, we ultimately aim at building a numerical infrastructure for the combined use of cryoET, intracellular nanotools and live cell imaging to resolve dynamic cellular processes with atomic resolution.

Group members
PhD Student
CSIC Scientist

Read the article

Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A
Architecture of the ESCPE-1 membrane coat
Nat Struct Mol Biol. 2023 Jul;30(7):958-969
doi: 10.1038/s41594-023-01014-7

Read the article

Talledge N, Yang H, Shi K, Coray R, Yu G, Arndt WG, Meng S, Baxter GC, Mendonça LM, Castaño-Díez D, Aihara H, Mansky LM, Zhang W
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation
J Mol Biol. 2023 Aug 1;435(15):168143
doi: 10.1016/j.jmb.2023.168143

Read the article

Zivanov J, Otón J, Ke Z, von Kügelgen A, Pyle E, Qu K, Morado D, Castaño-Díez D, Zanetti G, Bharat TAM, Briggs JAG, Scheres SHW
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
Elife. 2022 Dec 5;11:e83724
doi: 10.7554/eLife.83724

Read the article

S Scaramuzza, D Castaño-Díez

Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo.
PLoS Biol. 2021 Aug 26;19(8):e3001318.
DOI: 10.1371/journal.pbio.3001318

Read the article

PP Navarro, H Stahlberg, D Castaño-Díez.

Protocols for subtomogram averaging of membrane proteins in the Dynamo software package.
Front Mol Biosci. 2018 Sep 4:5:82
DOI: 10.3389/fmolb.2018.00082

Read the article

D Castaño-Díez, M Kudryashev, H Stahlberg

Dynamo catalogue: geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms.
J Struct Biol. 2017 Feb;197(2):135-144
DOI: 10.1016/j.jsb.2016.06.005