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Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / FARIAS ESTROZI Leandro

VEDA



Last updated : January 7, 2011
Comments/Questions : contact Gael Goret


The problem:

How to interpret low-resolution reconstructions of macromolecular assemblies (typically Transmission EM reconstructions) at atomic scale ?

The problem can be solved in the particular but frequent case where subunits are known at atomic scale (typically MX or NMR molecular models).


Our solution:
The main idea is to fit the available atomic models (considered as rigid bodies) into the EM reconstruction.

The method is to compare, the EM map with a calculated model-based electron density within a selected volume.

The numerical problem consists in determining and optimizing the variables that specify the positions of the rigid models within the macromolecular assembly.


What is VEDA ?
VEDA is a visual environment developed to fit interactively atomic models into 3D reconstructions. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used.


VEDA working !


Download and Install VEDA

VEDA_lin_64_Linux version 22-12-2010 (compiled with gfortran)
VEDA_lin_32_Linux version 22-12-2010 (compiled with gfortran)
Installation Guide (for Linux Ubuntu)
User Guide (Beta Version)
For some examples Please contact Gael Goret

Papers citing VEDA (last update 09/02/2015):

[1] J. Agirre, G. Goret, M. LeGoff, R. Sánchez-Eugenia, G. Marti, J. Navaza, D. Guérin, and E. Neumann. Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly. Journal of General Virology, 94(Pt 5):1058-1068, 2013.

[2] H. A. AL-Khayat, R. W. Kensler, J. M. Squire, S. B. Marston, and E. P. Morris. Atomic model of the human cardiac muscle myosin filament. Proceedings of the National Academy of Sciences, 110(1):318-323, 2013.

[3] H. A. AL-Khayata, R. W. Kenslerb, J. M. Squirec, S. B. Marstona, and E. P. Morrisd. Atomic model of the human cardiac muscle.

[4] R. Aramayo, M. Sherman, K. Brownless, R. Lurz, A. Okorokov, and E. Orlova. Biron-birkbeck institutional research online. Nucleic Acids Research, 39(20):8960-8971, 2011.

[5] R. Aramayo, M. B. Sherman, K. Brownless, R. Lurz, A. L. Okorokov, and E. V. Orlova. Quaternary structure of the specific p53-dna complex reveals the mechanism of p53 mutant dominance. Nucleic acids research, page gkr386, 2011.

[6] H.-S. Dai, Z. Liu, W. Jiang, and R. J. Kuhn. Directed evolution of a virus exclusively utilizing human epidermal growth factor receptor as the entry receptor. Journal of virology, 87(20):11231-11243, 2013.

[7] A. Desfosses, G. Goret, L. F. Estrozi, R. W. Ruigrok, and I. Gutsche. Nucleoprotein-rna orientation in the measles virus nucleocapsid by three-dimensional electron microscopy. Journal of virology, 85(3):1391-1395, 2011.

[8] A. Desfosses, E. A. Ribeiro Jr, G. Schoehn, D. Blondel, D. Guilligay, M. Jamin, R. W. Ruigrok, and I. Gutsche. Self-organization of the vesicular stomatitis virus nucleocapsid into a bullet shape. Nature communications, 4:1429, 2013.

[9] K. El Omari, G. Sutton, J. J. Ravantti, H. Zhang, T. S. Walter, J. M. Grimes, D. H. Bamford, D. I. Stuart, and E. J. Mancini. Plate tectonics of virus shell assembly and reorganization in phage phi8, a distant relative of mammalian reoviruses. Structure, 21(8):1384-1395, 2013.

[10] L. F. Estrozi, E. C. Settembre, G. Goret, B. McClain, X. Zhang, J. Z. Chen, N. Grigorieff, and S. C. Harrison. Location of the dsrnadependent polymerase, vp1, in rotavirus particles. Journal of molecular biology, 425(1):124-132, 2013.

[11] G. Goret. Recalage exible de modèles moléculaires dans les reconstructions 3D de microscopie électronique. PhD thesis, Grenoble, 2011.

[12] J. Lai-Kee-Him, P. Schellenberger, C. Dumas, E. Richard, S. Trapani, V. Komar, G. Demangeat, C. Ritzenthaler, and P. Bron. The backbone model of the arabis mosaic virus reveals new insights into functional domains of nepovirus capsid. Journal of structural biology, 182(1):1-9, 2013.

[13] J. R. López-Blanco and P. Chacón. Structural modeling from electron microscopy data. Wiley Interdisciplinary Reviews: Computational Molecular Science, 5(1):62-81, 2015.

[14] M. Magali, W. Stephanie, R. Aurelie, F. Daphna, S. Guy, E. Christine, C. Jacques, and G. Jean. The oligomer plasticity of the small heat-shock protein lo18 from oenococcus oeni infuences its role in both membrane stabilization and protein protection. Biochemical Journal, 444(1):97-104, 2012.

[15] M. Maitre. Le chaperon moleculaire Lo18 de Oenococcus oeni: caracterisation de ses activites en lien avec sa plasticite oligomerique. PhD thesis, Universite de Bourgogne, 2012.

[16] I. Rissanen, J. M. Grimes, A. Pawlowski, S. Mäntynen, K. Harlos, J. K. Bamford, and D. I. Stuart. Bacteriophage p23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage. Structure, 21(5):718-726, 2013.

[17] M. Stelter, I. Gutsche, U. Kapp, A. Bazin, G. Bajic, G. Goret, M. Jamin, J. Timmins, and L. Terradot. Architecture of a dodecameric bacterial replicative helicase. Structure, 20(3):554-564, 2012.

[18] D. Veesler, G. Robin, J. Lichière, I. Auzat, P. Tavares, P. Bron, V. Campanacci, and C. Cambillau. Crystal structure of bacteriophage spp1 distal tail protein (gp19. 1) a baseplate hub paradigm in gram-positive infecting phages. Journal of Biological Chemistry, 285(47):36666-36673, 2010.

[19] X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, et al. A sensor-adaptor mechanism for enterovirus uncoating from structures of ev71. Nature structural & molecular biology, 19(4):424-429, 2012.

[20] H. O. Yeung, A. Förster, C. Bebeacua, H. Niwa, C. Ewens, C. McKeown, X. Zhang, and P. S. Freemont. Inter-ring rotations of aaa atpase p97 revealed by electron cryomicroscopy. Open biology, 4(3):130142, 2014.