Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 384

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions

Open access
Cardone, Giovanni, Heymann, J. Bernard, Steven, Alasdair C.·2013·Journal of Structural Biology
DOI 10.1016/j.jsb.2013.08.002
Open this paper in CoChat — free account

Abstract

The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.jsb.2013.08.002

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 3 references

Research works printed but not linked: 45

  1. Bai, 2012, Cryo-EM structure of a 3D DNA-origami object, Proc. Natl. Acad. Sci. USA, 109, 20012, 10.1073/pnas.1215713109 · DOI · Paper page
  2. Baxter, 2009, Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules, J. Struct. Biol., 166, 126, 10.1016/j.jsb.2009.02.012 · DOI
  3. Beck, 2012, Near-atomic resolution structural model of the yeast 26S proteasome, Proc. Natl. Acad. Sci. USA, 109, 14870, 10.1073/pnas.1213333109 · DOI · Paper page
  4. Belnap, 2003, Diversity of core antigen epitopes of hepatitis B virus, Proc. Natl. Acad. Sci. USA, 100, 10884, 10.1073/pnas.1834404100 · DOI
  5. Cardone, 2005, A resolution criterion for electron tomography based on cross-validation, J. Struct. Biol., 151, 117, 10.1016/j.jsb.2005.04.006 · DOI
  6. Cardone, 2009, Visualization of a missing link in retrovirus capsid assembly, Nature, 457, 694, 10.1038/nature07724 · DOI
  7. Cardone, 2012, Procapsid assembly, maturation, nuclear exit: dynamic steps in the production of infectious herpesvirions, Adv. Exp. Med. Biol., 726, 423, 10.1007/978-1-4614-0980-9_19 · DOI
  8. Crowther, 1981, Assembly and packing of clathrin into coats, J. Cell Biol., 91, 790, 10.1083/jcb.91.3.790 · DOI
  9. Fernandez, 2008, Sharpening high resolution information in single particle electron cryomicroscopy, J. Struct. Biol., 164, 170, 10.1016/j.jsb.2008.05.010 · DOI
  10. Frank, 1975, Signal-to-noise ratio of electron micrographs obtained by cross correlation, Nature, 256, 376, 10.1038/256376a0 · DOI
  11. Frank, 1981, Computer averaging of electron micrographs of 40S ribosomal subunits, Science, 214, 1353, 10.1126/science.7313694 · DOI
  12. Gao, 2004, Dynamics of EF–G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset, J. Struct. Biol., 147, 283, 10.1016/j.jsb.2004.02.008 · DOI
  13. Harauz, 1986, Exact filters for general geometry three-dimensional reconstruction, Optik, 73, 146
  14. Harris, 1978, On the use of windows for harmonic analysis with the discrete Fourier transform, Proc. IEEE, 66, 51, 10.1109/PROC.1978.10837 · DOI · Paper page
  15. Harris, 2006, Epitope diversity of hepatitis B virus capsids: quasi-equivalent variations in spike epitopes and binding of different antibodies to the same epitope, J. Mol. Biol., 355, 562, 10.1016/j.jmb.2005.10.035 · DOI
  16. Hashem, 2013, Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29, Cell, 153, 1108, 10.1016/j.cell.2013.04.036 · DOI
  17. Hashem, 2013, High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome, Nature, 494, 385, 10.1038/nature11872 · DOI
  18. Heymann, 2007, Bsoft: image processing and molecular modeling for electron microscopy, J. Struct. Biol., 157, 3, 10.1016/j.jsb.2006.06.006 · DOI · Paper page
  19. Heymann, 2005, Visualization of the binding of Hsc70 ATPase to clathrin baskets: implications for an uncoating mechanism, J. Biol. Chem., 280, 7156, 10.1074/jbc.M411712200 · DOI
  20. Hinman, B., Bernstein, J., Staelin, D. 1984. Short-space Fourier transform image processing. In: IEEE International Conference on Acoustics, Speech and Signal Processing, vol. 9, IEEE, San Diego, CA, pp. 166–169. · DOI
  21. Huiskonen, 2004, The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes, Nat. Struct. Mol. Biol., 11, 850, 10.1038/nsmb807 · DOI
  22. Ishikawa, 2004, The N-terminal substrate-binding domain of ClpA unfoldase is highly mobile and extends axially from the distal surface of ClpAP protease, J. Struct. Biol., 146, 180, 10.1016/j.jsb.2003.11.018 · DOI
  23. Jenner, 2010, Structural aspects of messenger RNA reading frame maintenance by the ribosome, Nat. Struct. Mol. Biol., 17, 555, 10.1038/nsmb.1790 · DOI · Paper page
  24. Kessel, 1985, The structure of the stalk surface layer of a brine pond microorganism: correlation averaging applied to a double layered lattice structure, J. Microsc., 139, 63, 10.1111/j.1365-2818.1985.tb04662.x · DOI
  25. Kingston, 2000, Structure and self-association of the Rous sarcoma virus capsid protein, Structure, 8, 617, 10.1016/S0969-2126(00)00148-9 · DOI · Paper page
  26. Lasker, 2012, Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proc. Natl. Acad. Sci. USA, 109, 1380, 10.1073/pnas.1120559109 · DOI · Paper page
  27. LeBarron, 2008, Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome, J. Struct. Biol., 164, 24, 10.1016/j.jsb.2008.05.007 · DOI
  28. Leschziner, 2007, Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions, Annu. Rev. Biophys. Biomol. Struct., 36, 43, 10.1146/annurev.biophys.36.040306.132742 · DOI
  29. Liao, 2010, Definition and estimation of resolution in single-particle reconstructions, Structure, 18, 768, 10.1016/j.str.2010.05.008 · DOI
  30. Lin, 2011, An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles, J. Virol., 85, 9974, 10.1128/JVI.05013-11 · DOI
  31. Ludtke, 1999, EMAN: semiautomated software for high-resolution single-particle reconstructions, J. Struct. Biol., 128, 82, 10.1006/jsbi.1999.4174 · DOI
  32. Marles-Wright, 2008, Molecular architecture of the “stressosome”, a signal integration and transduction hub, Science, 322, 92, 10.1126/science.1159572 · DOI
  33. Penczek, 2002, Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms, J. Struct. Biol., 138, 34, 10.1016/S1047-8477(02)00033-3 · DOI
  34. Penczek, 2006, Estimation of variance in single-particle reconstruction using the bootstrap technique, J. Struct. Biol., 154, 168, 10.1016/j.jsb.2006.01.003 · DOI
  35. Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 · DOI · Paper page
  36. Purdy, 2008, Critical role of conserved hydrophobic residues within the major homology region in mature retroviral capsid assembly, J. Virol., 82, 5951, 10.1128/JVI.00214-08 · DOI
  37. Saxton, 1982, The correlation averaging of a regularly arranged bacterial cell envelope protein, J. Microsc., 127, 127, 10.1111/j.1365-2818.1982.tb00405.x · DOI · Paper page
  38. Sousa, 2007, Ab initio resolution measurement for single particle structures, J. Struct. Biol., 157, 201, 10.1016/j.jsb.2006.08.003 · DOI
  39. Stewart, 2000, Digitally collected cryo-electron micrographs for single particle reconstruction, Microsc. Res. Technol., 49, 224, 10.1002/(SICI)1097-0029(20000501)49:3<224::AID-JEMT2>3.0.CO;2-0 · DOI
  40. Stolken, 2011, Maximum likelihood based classification of electron tomographic data, J. Struct. Biol., 173, 77, 10.1016/j.jsb.2010.08.005 · DOI
  41. Trabuco, 2008, Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics, Structure, 16, 673, 10.1016/j.str.2008.03.005 · DOI · Paper page
  42. Trus, 2007, Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids, Mol. Cell, 26, 479, 10.1016/j.molcel.2007.04.010 · DOI
  43. Unser, 1987, A new resolution criterion based on spectral signal-to-noise ratios, Ultramicroscopy, 23, 39, 10.1016/0304-3991(87)90225-7 · DOI
  44. Unser, 2005, Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions, J. Struct. Biol., 149, 243, 10.1016/j.jsb.2004.10.011 · DOI
  45. van Heel, 1987, Similarity measures between images, Ultramicroscopy, 48, 95, 10.1016/0304-3991(87)90010-6 · DOI · Paper page

Cited by

Metadata

Authors
Cardone, G., Heymann, J. B., & Steven, A. C.
Venue
Journal of Structural Biology
Publisher
Elsevier BV
Published
2013-11
Volume
184
Issue
2
Pages
226-236
ISSN
1047-8477 (ISSN-L)
DOI
10.1016/j.jsb.2013.08.002
OpenAlex
W2034484189
Cited by
384
References
3
FWCI
5.67
Type
journal article
Language
en
Open access
green
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Funders
Intramural Research Program

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.