57 research outputs found
Map challenge: Analysis using a pair comparison method based on Fourier shell correlation
This document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differencesThe authors would like to acknowledge economical support from: The Spanish Ministry of Economy and Competitiveness through Grants BIO2013-44647-R, BIO2016-76400-R(AEI/FEDER, UE) and AEI/FEDER BFU 2016 74868P, the Comunidad Autónoma de Madrid through Grant: S2017/BMD-3817, European Union (EU) and Horizon 2020 through grant CORBEL (INFRADEV-1-2014-1, Proposal: 654248). This work used the EGI Infrastructure and is co-funded by the EGI-Engage project (Horizon 2020) under Grant No. 654142. European Union (EU) and Horizon 2020 through grant West-Life (EINFRA-2015-1, Proposal: 675858) European Union (EU) and Horizon 2020 through grant Elixir - EXCELERATE (INFRADEV-3-2015, Proposal: 676559) European Union (EU) and Horizon 2020 through grant iNEXT (INFRAIA-1–2014-2015, Proposal: 653706). The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI projec
Transfer function restoration in 3D electron microscopy via iterative data refinement
Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, the 3D reconstructions performed with these CTF-affected projections are also affected by an implicit 3D transfer function. For high-resolution electron microscopy, the effect of the CTF is quite dramatic and limits severely the achievable resolution. In this work we make use of the iterative data refinement (IDR) technique to ameliorate the effect of the CTF. It is demonstrated that the approach can be successfully applied to noisy data.Partial support is acknowledged to the Comisión Interministerial de Ciencia y Tecnología
of Spain through projects BIO98-0761 and BIO2001-1237 and to National Institutes of
Health through grant HL70472. The work of Y. Censor was done in part at the Center
for Computational Mathematics and Scientific Computation (CCMSC) at the University
of Haifa and supported by Research Grant 592/00 from the Israel Science Foundation
founded by the Israel Academy of Sciences and Humanities
On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy
This work was funded by the Spanish Ministerio de
Economía y Competividad through grants BFU2009-09331,
BIO2010-16566, ACI2009-1022, ACI2010-1088 and AIC-A-
2011-0638, by the Comunidad Autonoma de Madrid through
grant S2010/BMD-2305, by NFS grant No. 1114901 and by the
Spanish National Institute of Bioinformatics (a project funded
by the Instituto de Salud Carlos III). This work was conducted
using the Protégé resource, which is supported by grant
LM007885 from the United States National Library of
Medicine. COSS is a Ramón y Cajal researcher financed by the European Social Fund and the Ministerio de Economía y
Competitividad. JV is a Juan de la Cierva Postdoctoral Fellow
(JCI-2011-10185). This work was funded by Instruct, which
is part of the European Strategy Forum on Research Infrastructures
(ESFRI) and is supported by national member
subscriptions
Consistent and elastic registration of histological sections using vector-spline regularization
The final publication is available at Springer via http://dx.doi.org/10.1007/11889762_8Revised Papers on Second International ECCV Workshop, CVAMIA 2006 Graz, Austria, May 12, 2006Here we present a new image registration algorithm for the alignment of histological sections that combines the ideas of B-spline based elastic registration and consistent image registration, to allow simultaneous registration of images in two directions (direct and inverse). In principle, deformations based on B-splines are not invertible. The consistency term overcomes this limitation and allows registration of two images in a completely symmetric way. This extension of the elastic registration method simplifies the search for the optimum deformation and allows registering with no information about landmarks or deformation regularization. This approach can also be used as the first step to solve the problem of group-wise registration.Ignacio Arganda-Carreras is being supported by a predoctoral FPI-CAM fellow-
ship since October 2003. Carlos Ortiz-de-Solorzano is supported by a Ramon y
Cajal (Spanish Ministry of Education and Science ryc-2004-002353) and a Marie
Curie International Reintegration Grant (FP6-518688). Jan Kybic was sponsored
by the Czech Ministery of Education under project number MSM210000012. Par-
tial support is acknowledged to Comunidad de Madrid through grant GR/SAL/0234,
to Instituto de Salud Carlos III-Fondo de Investigaciones Sanitarias (FIS) through
the IM3 Network and grant 040683 and to the Plan Nacional de Investigación
Científica, Desarrollo e Innovación Tecnológica (I+D+I)
Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses
Enteric adenoviruses, one of the main causes of viral gastroenteritis in the world, must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be different from that of other adenoviruses. We report the 4-Å-resolution structure of a human enteric adenovirus, HAdV-F41, and compare it with that of other adenoviruses with respiratory (HAdV-C5) and ocular (HAdV-D26) tropisms. While the overall structures of hexon, penton base, and internal minor coat proteins IIIa and VIII are conserved, we observe partially ordered elements reinforcing the vertex region, which suggests their role in enhancing the physicochemical capsid stability of HAdV-F41. Unexpectedly, we find an organization of the external minor coat protein IX different from all previously characterized human and nonhuman mastadenoviruses. Knowledge of the structure of enteric adenoviruses provides a starting point for the design of vectors suitable for oral delivery or intestinal targetingThis work was supported by grants PID2019-104098GB-I00/AEI/10.13039/501100011033 and BFU2016-74868-P, cofunded by the Spanish State Research Agency and the European Regional Development Fund; BFU2013-41249-P and BIO2015-68990-REDT (the Spanish Adenovirus Network, AdenoNet) from the Spanish Ministry of Economy, Industry, and Competitiveness; and the Agencia Estatal CSIC (2019AEP045) to C.S.M. The CNB-CSIC is further supported by a Severo Ochoa Excellence grant (SEV 2017-0712). Work in M.B’s. lab was supported by grant 194562-08 from the Natural Sciences and Engineering Research Council of is a recipient of a Juan de la Cierva postdoctoral contract funded by the Spanish State Research Agency. M.P.-I. holds a predoctoral contract from La Caixa Foundation (ID 100010434), under agreement LCF/BQ/SO16/52270032. Access to CEITEC was supported by iNEXT, project number 653706, funded by the Horizon 2020 Programme of the European Union. The CEITEC Cryo-electron Microscopy and Tomography core facility is supported by MEYS CR (LM2018127
MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography
Open Access funded by Medical Research CouncilThe MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages. Following extensive discussions, the authors, who represent leading software packages in the field, propose a set of extensions to the MRC format standard designed to accommodate these variants, while restoring interoperability. The MRC format is equivalent to the map format used in the CCP4 suite for macromolecular crystallography, and the proposal also maintains interoperability with crystallography software. This Technical Note describes the proposed extensions, and serves as a reference for the standard.We thank Chris Booth and Steffen Meyer from Gatan Inc. for
clarifying the format definition used by Digital Micrograph.
Acknowledgement for support from National Institute of Health,
USA includes: NIGMS grant P41GM103310 (AC and SD), NIBIB
grant 5R01-EB005027 (DM), and R01GM080139 (SJL). RH and
MW would like to thank the UK Medical Research Council for the
award of Partnership Grant MR/J000825/1 to support the establishment
of CCP-EM. RH and JS are also supported by MRC grant
U105184322
FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation
In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure “FSC-Q”, and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atomsWe thank Prof. David Veesler for providing us the half maps of the spike glycoprotein of SARS-CoV-2. The authors would like to acknowledge financial support from: the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish National Research Council (PIE/COVID-19 number 202020E079), the Spanish Ministry of Economy and Competitiveness through grants SEV 2017-0712, PID2019-104757RB-I00/AEI/10.13039/501100011033, the Instituto de Salud Carlos III through grant PT17/0009/0010 (ISCIII-GEFI/ERDF-). Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. UE H2020 grant HighResCells (ERC-2018-SyG, Proposal: 810057). This work was supported by the Intramural Research Program of the National Institute for Arthritis, musculoskeletal, and Skin Diseases, NIH. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI projec
Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited
Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps.We thank Dr. Llorca for his support during the acquisition of the C3b images and Dr. Shaikh for his support in the use of Spider for the RCT reconstructions. The authors would like to acknowledge economical support from the Spanish Ministry of Economy and Competitiveness through grants AIC-A-2011-0638 and BIO2013-44647-R, the Comunidad de Madrid through grant CAM (S2010/BMD-2305), as well as a postdoctoral Juan de la Cierva grant with reference JCI-2011-10185 to Javier Vargas. Vahid Abrishami is a holder of La Caixa scholarship and C.O.S. Sorzano is recipient of a Ramon y Cajal fellowship
Structure and uncoating of immature adenovirus
Maturation via proteolytical processing is a common trait in the viral world, and is
often accompanied by large conformational changes and rearrangements in the capsid.
The adenovirus protease has been shown to play a dual role in the viral infectious
cycle: (a) in maturation, as viral assembly starts with precursors to several of the
structural proteins, but ends with proteolytically processed versions in the mature
virion; and (b) in entry, because protease-impaired viruses have difficulties in
endosome escape and uncoating. Indeed, viruses that have not undergone proteolytical
processing are not infectious. We present the 3D structure of immature adenovirus
particles, as represented by the thermosensitive mutant Ad2 ts1 grown under nonpermissive
conditions, and compare it with the mature capsid. Our 3DEM maps at
subnanometer resolution indicate that adenovirus maturation does not involve large
scale conformational changes in the capsid. Difference maps reveal the location of
unprocessed peptides pIIIa and pVI and help to define their role in capsid assembly
and maturation. An intriguing difference appears in the core, indicating a more
compact organization and increased stability of the immature cores. We have further
investigated these properties by in vitro disassembly assays. Fluorescence and
electron microscopy experiments reveal differences in the stability and uncoating of
immature viruses, both at the capsid and core levels, as well as disassembly
intermediates not previously imaged.This work was supported by grants from the Ministerio de Ciencia e Innovación of Spain (BFU2007-60228 to C.S.M. and BIO2007-67150-C03-03 to R.M.), the Comunidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas (CCG08-CSIC/SAL-3442 to C.S.M.) and the National Institutes of Health (5R01CA111569 to D.T.C., R0141599 to W.F.M. and GM037705 to S.J.F.). R.M.-C. is a recipient of a PFIS fellowship from the Instituto de Salud Carlos III of Spain. A.J.P.-B. holds a CSIC JAE-Doc postdoctoral position, partially funded by the European Social FundPeer reviewe
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