National Center for Macromolecular Imaging

Journal and Book Covers by NCMI Researchers


February 2011

Journal of Virology View Article
Seeing the Portal in Herpes Simplex Virus Type 1 B Capsids

Rochat, R. H.; Liu, X.; Murata, K.; Nagayama, K.; Rixon, F. J.; Chiu, W.

Journal of Virology , Volume 85 (4): 1871
American Society For Microbiology – Feb 15, 2011
December 2010

Journal of Molecular Biology View Article
Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography

Yasuyuki Miyazaki, Rossitza N. Irobalieva, Blanton S. Tolbert, Adjoa Smalls-Mantey, Kilali Iyalla, Kelsey Loeliger, Victoria D’Souza, Htet Khant, Michael F. Schmid, Eric L. Garcia, Alice Telesnitsky, Wah Chiu, Michael F. Summers
October 2010

NIAID Sponsered Workshop
Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and Cellular Structures
October 2010

Journal of Molecular Biology View Article
Visualizing the Structural Changes of Bacteriophage Epsilon15 and Its Salmonella Host during Infection

Juan T. Chang, Michael F. Schmid, Cameron Haase-Pettingell, Peter R. Weigele, Jonathan A. King, Wah Chiu
July 2010

Nature Structural & Molecular Biology View Article
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus

Xiangan Liu, Qinfen Zhang, Kazuyoshi Murata, Matthew L Baker, Matthew B Sullivan, Caroline Fu, Matthew T Dougherty, Michael F Schmid, Marcia S Osburne, Sallie W Chisholm & Wah Chiu
January 2008

Physics Today View Article
"Cryo-Electron Microscopy of Biological Nanostructures", Physics Today, January 2008, Volume 62, Issue 1, pp. 48-54.
October 2007

Journal of Structural Biology View Article
Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm

J Struct Biol. 2007 Oct;160(1):11-27

Xiangan Liu, Wen Jiang, Joanita Jakana and Wah Chiu
February 2007

J. Mol. Biol. View Article
Genome sequence, structural proteins, and capsid organization of the cyanophage syn5: a "horned" bacteriophage of marine synechococcus.

Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, King J.

J Mol Biol. 2007 May 11;368(4):966-81. Epub 2007 Feb 22.Click here to read
February 2007

J. Virology View Article
Electron Cryotomography Reveals the Portal in the Herpesvirus Capsid

Juan T. Chang, Michael F. Schmid, Frazer J. Rixon, and Wah Chiu

Journal of Virology, February 2007, p. 2065-2068, Vol. 81, No. 4
January 2007

Journal of Structural Biology
Cover image only.
July 2006

JEOL news
Visualization of Biological Nano-Machines at Subnanometer Resolutions

W. Chiu, D. Chen, J. Jakana, J. Chang, W. Jiang, S. Ludtke, and M. Baker

JEOL News, Vol. 41 No. 1, pp. 12 - 17
March 2006

Nature Structural & Molecular Biology View Article
Arac D, Chen X, Khant HA, Ubach J, Ludtke SJ, Kikkawa M, Johnson AE, Chiu W, Sudhof TC, Rizo J.

Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids.

Nat Struct Mol Biol. 2006 Mar;13(3):209-17. Epub 2006 Feb 19.
February 2006

Nature View Article
Jiang W, Chang J, Jakana J, Weigele P, King J, Chiu W.

Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.
Nature. 2006 Feb 2;439(7076):612-6.
September 2005

PLos Computational Biology View Article
J. Carson, T. Ju, H. Lu, C. Thaller, M. Xu, S. Pallas, M. Crair, J. Warren, W. Chiu, G. Eichele

A Digital Atlas to Characterize the Mouse Brain Transcriptome

PLoS Computational Biology, September 2005, Volume 1, Issue 4, pp. 289-296

August 2004

NCRR Reporter, Summer 2004 View Article
A Closer Look at the Bigger Picture
Integrated technologies examine the middle ground between atomic details and whole cells.
August 2004

Journal of Structural Biology View Article
Booth, C.R., Jiang W., Baker M.L., Zhou Z.H., Ludtke S.J., Chiu W.,
A 9 Single Particle Reconstruction From CCD Captured Images On A 200
kV Electron Cryomicroscope.
Journal Of Structural Biology, 147 (2004) 116,127

Sub-nanometer resolution structure determination is becoming a common
practice in electron cryomicroscopy of macromolecular assemblies. The
data for these studies have until now been collected on photographic
film. Using cytoplasmic polyhedrosis virus (CPV), a previously
determined structure, as a test specimen, we show the feasibility of
obtaining a 9 structure from images acquired from a 4 k 4 k Gatan
CCD on a 200 kV electron cryomicroscope. The match of the small alpha,
Greek-helices in the protein components of the CPV with the previous
structure of the same virus validates the suitability of this type of
camera as the recording media targeted for single particle
reconstructions at sub-nanometer resolution.
February 2004

Developmental Biology View Article
Malgorzata Kloca, Szczepan Bilinskib, Matthew T. Doughertyc, Eric M. Breyd, e and Laurence D. Etkin, Developmental Biology 266 (2004) 43 61

Little is known about the formation of germline cyst and the differentiation of oocyte within the cyst in vertebrates. In the majority of invertebrates in the initial stages of gametogenesis, male and female germ cells develop in full synchrony as a syncytia of interconnected cells called germline cysts (clusters, nests). Using electron microscopy, immunostaining and three-dimensional reconstruction, we were able to elucidate the process of cyst formation in the developing ovary of the vertebrate Xenopus laevis. We found that the germline cyst in Xenopus contains 16 cells that are similar in general architecture and molecular composition to the cyst in Drosophila. Nest cells are connected by cytoplasmic bridges that contain ring canal-like structures. The nest cells contain a structure similar to the Drosophila fusome that that is probably involved in anchoring of the centrioles and organization of the primary mitochondrial cloud (PMC) around the centriole. We also find that in contrast to other organisms, in Xenopus, apoptosis is a rare event within the developing ovary. Our studies indicate that the processes responsible for the formation of female germline cysts and the establishment of germ cell polarity are highly conserved between invertebrates and vertebrates. The dissimilarities between Drosophila and Xenopus and the uniqueness of each system probably evolved through modifications of the same fundamental design of the germline cyst.
June 2003

Structure View Article
Cytoplasmic polyhedrosis virus structure at 8 A by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation.
Zhou ZH, Zhang H, Jakana J, Lu XY, Zhang JQ

The single-shelled cytoplasmic polyhedrosis virus (CPV) is a unique member of the Reoviridae. Despite lacking protective outer shells, it exhibits striking capsid stability and is capable of endogenous RNA transcription and processing. The 8 A three-dimensional structure of CPV by electron cryomicroscopy reveals secondary structure elements present in the capsid proteins CSP, LPP, and TP, which have alpha+beta folds. The extensive nonequivalent interactions between CSP and LPP, the unique CSP protrusion domain, and the perfect inter-CSP surface complementarities may account for the enhanced capsid stability. The slanted disposition of TP functional domains and the stacking of channel constrictions suggest an iris diaphragm-like mechanism for opening/closing capsid pores and turret channels in regulating the highly coordinated steps of mRNA transcription, processing, and release.
February 2003

Nature Structural Biology View Article
Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions
Wen Jiang, Zongli Li, Zhixian Zhang, Matthew L. Baker, Peter E. Prevelige Jr. & Wah Chiu
Nature Structural Biology 10, 131 - 135 (01 Feb 2003)

Bacteriophage P22 is a prototypical biological machine used for studying protein complex assembly and capsid maturation. Using cryo-EM, we solved the structures of P22 before and after the capsid maturation at 8.5 and 9.5 resolutions, respectively. These structures allowed visualization of -helices and -sheets from which the capsid protein fold is derived. The capsid fold is similar to that of the coat protein of HK97 bacteriophage. The cryo-EM shows that a large conformational change of the P22 capsid during maturation transition involves not only the domain movement of individual subunits, but also refolding of the capsid protein
January 2003

Journal of Virology View Article
Paredes A, Alwell-Warda K, Weaver SC, Chiu W, Watowich SJ.
Structure of isolated nucleocapsids from venezuelan equine encephalitis virus and implications for assembly and disassembly of enveloped virus.
J Virol. 2003 Jan; 77(1): 659-64.

Venezuelan equine encephalitis virus (VEEV) is an important human and equine pathogen in the Americas, with widespread reoccurring epidemics extending from South America to the southern United States. Most troubling, VEEV has been made into a weapon by several countries and is currently restricted by the Centers for Disease Control and Prevention as a potential biological warfare and terrorism agent. To facilitate the development of antiviral compounds, the structure of the nucleocapsid isolated from VEEV has been determined by electron cryomicroscopy and image reconstruction and represents the first three-dimensional structure of a nucleocapsid isolated from a single-stranded enveloped RNA virus. The isolated VEEV nucleocapsid undergoes significant reorganization relative to its structure within VEEV. However, the isolated nucleocapsid clearly exhibits T=4 icosahedral symmetry, and its characteristic nucleocapsid hexons and pentons are preserved. The diameter of the isolated nucleocapsid is 11.5% larger than that of the nucleocapsid within VEEV, with radial expansion being greatest near the hexons. Significantly, this is the first direct structural evidence showing that a simple enveloped virus undergoes large conformational changes during maturation, suggesting that the lipid bilayer and the transmembrane proteins of simple enveloped viruses provide the energy necessary to reorganize the nucleocapsid during maturation.
April 2002

Current Opinion in Structural Biology View Article
Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches, Pages 263-269
Wah Chiu, Matthew L. Baker, Wen Jiang and Z. Hong Zhou

Intermediate-resolution (79) structures of large macromolecular complexes can be obtained by electron cryomicroscopy. This structural information, combined with bioinformatics data for the individual protein components or domains, can lead to a fold model for the entire complex. Such approaches have been demonstrated with the 6.8 structure of the rice dwarf virus to derive models for the major capsid shell proteins
March 2002

Molecular Therapy View Article
Bilamellar Cationic Liposomes Protect Adenovectors from Preexisting Humoral Immune Responses, Molecular Therapy, Volume 5, Issue 3, March 2002, Pages 233-241
Patricia Yotnda, Dong-Hua Chen, Wah Chiu, Pedro A. Piedra, Alan Davis, Nancy Smyth Templeton and Malcolm K. Brenner

Adenoviral vectors have been widely used for gene therapy, but they are limited both by the presence of a humoral immune response that dramatically decreases the level of transduction after reinjection and by their requirement for target cells to express appropriate receptors such as Coxsackie adenovirus receptor (CAR). To overcome both limits, we encapsulated adenovectors using bilamellar DOTAP:chol liposomes. Electron micrography (EM) showed that these liposomes efficiently encapsulated the vectors, allowing CAR-independent adenovector transduction of otherwise resistant cells. DOTAP:chol-encapsulated adenovectors encoding LacZ or 1-antitrypsin inhibitor (AAT) were also functionally resistant ex vivo and in vivo to the neutralizing effects of human anti-adenoviral antibodies, unlike other liposomal systems. Hence, bilamellar DOTAP:chol liposomes may be useful for applications using adenovectors in which the target cells lack adenoviral receptors or in which the recipient already has or develops a neutralizing antibody response that would otherwise inactivate readministered vector.
January 2002

Developmental Biology View Article
Kloc, M., Dougherty, M.T., Bilinski, S., Chan, A.P., Brey, E., King, M.L., Patrick, C.W., Jr. & Etkin, L.D.
Three-dimensional ultrastructural analysis of RNA distribution within germinal granules of Xenopus.
Dev Biol 241 :79-93

The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. Serial EM sections were used to reconstruct a three-dimensional image of germinal granule distribution within the METRO region of the cloud and the distribution of RNAs on the granules in oocytes and embryos. We found that, in the oocytes, the majority of RNAs were associated either with the precursor of germinal granules or with the germ plasm matrix. Only Xcat2, Xpat, and DEADSouth RNAs were associated with the mature germinal granules in oocytes, while only Xcat2 and Xpat were associated with germinal granules in embryos. However, Xcat2 was the only RNA that was consistently sequestered inside the germinal granules, while the others were located on the periphery. Xdazl, which functions in germ cell migration/formation, was detected on the matrix between granules. Later in development, Xcat2 mRNA was released from the germinal granules. This coincides with the timing of its translational derepression. These results demonstrate that there is a dynamic three-dimensional architecture to the germinal granules that changes during oogenesis and development. They also indicate that association of specific RNAs with the germinal granules is not a prerequisite for their serving a germ cell function; however, it may be related to their state of translational repression.
October 2001

Nature Structural Biology View Article
Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus pp 868 - 873
Z. Hong Zhou, Matthew L. Baker, Wen Jiang, Matthew Dougherty, Joanita Jakana, Gang Dong, Guangying Lu & Wah Chiu

The three-dimensional structure of rice dwarf virus was determined to 6.8 resolution by single particle electron cryomicroscopy. By integrating the structural analysis with bioinformatics, the folds of the proteins in the double-shelled capsid were derived. In the outer shell protein, the uniquely orientated upper and lower domains are composed of similar secondary structure elements but have different relative orientations from that of bluetongue virus in the same Reoviridae family. Differences in both sequence and structure between these proteins may be important in defining virushost interactions. The inner shell protein adopts a conformation similar to other members of Reoviridae, suggesting a common ancestor that has evolved to infect hosts ranging from plants to animals. Symmetry mismatch between the two shells results in nonequivalent, yet specific, interactions that contribute to the stability of this large macromolecular machine.
June 2001

Journal of Molecular Biology View Article
Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid1, Pages 903-914
Jing He, Michael F. Schmid, Z. Hong Zhou, Frazer Rixon and Wah Chiu

A characteristic of virus assembly is the use of symmetry to construct a complex capsid from a limited number of different proteins. Many spherical viruses display not only icosahedral symmetry, but also local symmetries, which further increase the redundancy of their structural proteins. We have developed a computational procedure for evaluating the quality of these local symmetries that allows us to probe the extent of local structural variations among subunits. This type of analysis can also provide orientation parameters for carrying out non-icosahedral averaging of quasi-equivalent subunits during three-dimensional structural determination. We have used this procedure to analyze the three types of hexon (P, E and C) in the 8.5 resolution map of the herpes simplex virus type 1 (HSV-1) B capsid, determined by electron cryomicroscopy. The comparison of the three hexons showed that they have good overall 6-fold symmetry and are almost identical throughout most of their lengths. The largest difference among the three lies near the inner surface in a region of about 34 in thickness. In this region, the P hexon displays slightly lower 6-fold symmetry than the C and E hexons. More detailed analysis showed that parts of two of the P hexon subunits are displaced counterclockwise with respect to their expected 6-fold positions. The most highly displaced subunit interacts with a subunit from an adjacent P hexon (P'). Using the local 6-fold symmetry axis of the P hexon as a rotation axis, we examined the geometrical relationships among the local symmetry axes of the surrounding capsomeres. Deviations from exact symmetry are also found among these local symmetry axes. The relevance of these findings to the process of capsid assembly is considered.
May 2001

Journal of Molecular Biology View Article
Bridging the information gap: computational tools for intermediate resolution structure interpretation1, Pages 1033-1044
Wen Jiang, Matthew L. Baker, Steven J. Ludtke and Wah Chiu

Due to large sizes and complex nature, few large macromolecular complexes have been solved to atomic resolution. This has lead to an under-representation of these structures, which are composed of novel and/or homologous folds, in the library of known structures and folds. While it is often difficult to achieve a high-resolution model for these structures, X-ray crystallography and electron cryomicroscopy are capable of determining structures of large assemblies at low to intermediate resolutions. To aid in the interpretation and analysis of such structures, we have developed two programs: helixhunter and foldhunter. Helixhunter is capable of reliably identifying helix position, orientation and length using a five-dimensional cross-correlation search of a three-dimensional density map followed by feature extraction. Helixhunter's results can in turn be used to probe a library of secondary structure elements derived from the structures in the Protein Data Bank (PDB). From this analysis, it is then possible to identify potential homologous folds or suggest novel folds based on the arrangement of alpha helix elements, resulting in a structure-based recognition of folds containing alpha helices. Foldhunter uses a six-dimensional cross-correlation search allowing a probe structure to be fitted within a region or component of a target structure. The structural fitting therefore provides a quantitative means to further examine the architecture and organization of large, complex assemblies. These two methods have been successfully tested with simulated structures modeled from the PDB at resolutions between 6 and 12 A. With the integration of helixhunter and foldhunter into sequence and structural informatics techniques, we have the potential to deduce or confirm known or novel folds in domains or components within large complexes.
February 2001

Journal of Structural BIology View Article
Editorial, Page 89
Steven Ludtke and Wah Chiu
January 2001

Federal Funding for Biomedical and Related Life Sciences Research FY
The rapidly increasing quantity of DNA sequence data as well as the powerful technologies available to determine three-dimensional structures of proteins and protein complexes at the atomic level, will provide valuable information for use in rationalized drug design and the development of improved clinical treatments for disease and infection.
November 2000

Micron
Thuman-Commike, P.A. and Chiu, W.
Reconstruction principles of icosahedral virus structure determination using electron cryomicroscopy.
Micron 31 :687-711.
April 2000

Journal of Virology
Identification of additional coat-scaffoling interactions in a bacteriophage P22 mutatnt defective in maturation.
March 2000

Journal of Molecular Biology View Article
Visualization of the maturation transition in bacteriophage P22 by electron cryomicroscopy1, Pages 615-626
Zhixian Zhang, Barrie Greene, Pamela A. Thuman-Commike, Joanita Jakana, Peter E. Prevelige, Jr , Jonathan King and Wah Chiu
October 1999

Journal of Virology
A radially colored, shaded surface representation of shell protein densities of herpes simplex virus type 1 VP26- and VP5-VP19C particles shown in half. The VP26- capsid (left) is a T=16 particle of 1,250 in diameter and VP5-VP19C (right) is a T=7 particle of 880 in diameter.
September 1999

Trends in Cell Biology
A light micrograph immunostaining of cytoplasmic cofilin-actin rods that form in living cells in respsosnse to stress.
August 1999

Journal of Molecular Biology
An image of an actin filament exhibiting three cofilin-induced 'branches' and a mechanistic model of how these branches might contribute to catastrophic disassembly of F-actin.
July 1999

Virology
A three-dimensional structure of the intact human cytomegalovirus (HCMV) determined to an 18- resolution by electron cryomicroscopy and computer reconsruction. An icosahedrally ordered teguement layer formed by 960 copies of filamentous density is also visualized, which interacts with the pentons, hexons, and triplexes of the underlying capsid.
June 1999

Biophysical Journal
A schematic of partially assembled bacteriophage P22 procapsids with color coding denoting the quasi-equivalent coat protein subunits and black lines denoting the scaffolding protein.
April 1999

Journal of Virology
Visualization of tegument-capsid interactions and DNA in intact herpes simplex virus type 1 virions.
Zhou ZH, Chen DH, Jakana J, Rixon FJ, Chiu W.
J Virol. 1999 Apr;73(4):3210-8
February 1999

Journal of Virology
A three-dimensional structure of cytoplasmic polyhedrosis virus, a single-shelled member of the Reoviridae, was determined to 17- resolution from electron cryomicroscopy images. The full virus (top), which is color-coded according to particle radius, has a T=1 icosahedral capsid shell decorated with 12 characteristic pairs of concentric spikes at its vertices. Structural comparisons of the full and empty capsids have revealed ordered double-stranded RNA inside the full capsid (lower left, yellow and red) and its interactions with the transcriptional enzyme complexes (lower right).
September 1998

Ultramicroscopy
A single-unit cell versus correlation averaging image processing of gp32*I protein crystal images. Multivariate statistical analysis applied to single unit cells, extracted from an image of a crystal, allows to find subsets of unit cells and get more information from such an image.
January 1998

Biophysical Journal
A three-dimensional structures of bacteriophage P22 procapsids assembled in the absence of the scaffolding protein.
November 1997

Journal of Structural Biology
A montage of images from the "Biophysics of Microtubules" workshop held in 1996 at the NCMI.
January 1997

Structural Biology of Viruses
This book was co-edited by Wah Chiu, Roger Burnett, and Robert Garcea and published by Oxford University Press. Topics covered include: mechanisms of cell attachment and entry, principles of virus assembly, as well as virus structure determination by electron microscopy and X-ray crystallography.
July 1996

Journal of Molecular Biology
A three-dimensional reconstruction of the bacteriophage P22 determined to 19 resolution. The outer coat protein can be classified into four unique subunit conformations (highlighted).
October 1995

Journal of Structural Biology
A gallery of F-actin structures. From left to right: aA1-2/F-actin (courtesy of A. McGough), F-actin (courtesy of E. Egelman), thin filament decorated with myosin S1 (courtesy of R. Milligan), F-actin (courtesy of U. Aebi), and scruin/F-actin (courtesy of M. Schmid).
September 1994

Journal of Molecular Biology
A spot scan image of herpesvirus capsids (left) taken on the JEOL4000 cryomicroscope and three computationally extracted hexons (right) comprising the virus capsid.
July 1994

Journal of Structural Biology
An electron diffraction pattern from a crotoxin complex crystal embedded in glucose. The pattern shows reflections out to a resolution better than 3.
July 1994

Journal of Molecular Biology
A projection map of Bacillus stearothermophilus 50 S ribosomal subunits crystallized on phospholipid monolayers.
February 1994

The Journal of Cell Biology
A 13 resolution reconstruction of an actin/scruin filament which was computationally isolated from the acrosomal bundle of Limulus sperm. The reconstruction is in green with an atomic model of F-actin (red, white, and blue). The two actin subunits to which scruin binds are shown on the right.
August 1989

EMSA Bulletin
A reconstruction obtained from images of tobacco mosaic virus. From a bulletin published by the Electron Microscopy Society of America (now known as the Microscopy Society of America).