4udv: Difference between revisions

Revision as of 08:19, 22 March 2023

Cryo-EM structure of TMV at 3.35 A resolution

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Structural highlights

4udv is a 2 chain structure with sequence from Tobacco mosaic virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_TMV Capsid protein self-assembles to form rod-shaped virions about 18 nm in diameter with a central canal enclosing the viral genomic RNA.

Publication Abstract from PubMed

With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35A resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2A in resolution using cryo-EM.

Seeing tobacco mosaic virus through direct electron detectors.,Fromm SA, Bharat TA, Jakobi AJ, Hagen WJ, Sachse C J Struct Biol. 2014 Dec 17. pii: S1047-8477(14)00265-2. doi:, 10.1016/j.jsb.2014.12.002. PMID:25528571^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fromm SA, Bharat TA, Jakobi AJ, Hagen WJ, Sachse C. Seeing tobacco mosaic virus through direct electron detectors. J Struct Biol. 2014 Dec 17. pii: S1047-8477(14)00265-2. doi:, 10.1016/j.jsb.2014.12.002. PMID:25528571 doi:https://dx.doi.org/10.1016/j.jsb.2014.12.002

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Fromm SA, Bharat TA, Jakobi AJ, Hagen WJ, Sachse C. Seeing tobacco mosaic virus through direct electron detectors. J Struct Biol. 2014 Dec 17. pii: S1047-8477(14)00265-2. doi:, 10.1016/j.jsb.2014.12.002. PMID:25528571 doi:https://dx.doi.org/10.1016/j.jsb.2014.12.002

[1]

@@ Line 3: / Line 3: @@
 <SX load='4udv' size='340' side='right' viewer='molstar' caption='[[4udv]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4udv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Tobacco_mosaic_virus Tobacco mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UDV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4UDV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4udv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Tobacco_mosaic_virus Tobacco mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UDV FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4udv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4udv OCA], [http://pdbe.org/4udv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4udv RCSB], [http://www.ebi.ac.uk/pdbsum/4udv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4udv ProSAT]</span></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4udv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4udv OCA], [https://pdbe.org/4udv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4udv RCSB], [https://www.ebi.ac.uk/pdbsum/4udv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4udv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CAPSD_TMV CAPSD_TMV]] Capsid protein self-assembles to form rod-shaped virions about 18 nm in diameter with a central canal enclosing the viral genomic RNA.
+[https://www.uniprot.org/uniprot/CAPSD_TMV CAPSD_TMV] Capsid protein self-assembles to form rod-shaped virions about 18 nm in diameter with a central canal enclosing the viral genomic RNA.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 27: @@
 [[Category: Large Structures]]
 [[Category: Tobacco mosaic virus]]
-[[Category: Bharat, T A.M]]
+[[Category: Bharat TAM]]
-[[Category: Fromm, S A]]
+[[Category: Fromm SA]]
-[[Category: Hagen, W J.H]]
+[[Category: Hagen WJH]]
-[[Category: Jakobi, A J]]
+[[Category: Jakobi AJ]]
-[[Category: Sachse, C]]
+[[Category: Sachse C]]
-[[Category: Direct electron detector]]
-[[Category: High resolution]]
-[[Category: Single particle helical reconstruction]]
-[[Category: Viral protein]]

4udv: Difference between revisions

Revision as of 08:19, 22 March 2023

Cryo-EM structure of TMV at 3.35 A resolution

Structural highlights

Function

Publication Abstract from PubMed

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References

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