5m3l: Difference between revisions

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'''Unreleased structure'''


The entry 5m3l is ON HOLD
==Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin==
<SX load='5m3l' size='340' side='right' viewer='molstar' caption='[[5m3l]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5m3l]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Lumbricus_terrestris Lumbricus terrestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M3L FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=5m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3l OCA], [https://pdbe.org/5m3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m3l RCSB], [https://www.ebi.ac.uk/pdbsum/5m3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3l ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLB4_LUMTE GLB4_LUMTE]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of approximately 3.8 A is presented as an example of the use of the ABC-4D procedure.


Authors:  
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.,Afanasyev P, Seer-Linnemayr C, Ravelli RBG, Matadeen R, De Carlo S, Alewijnse B, Portugal RV, Pannu NS, Schatz M, van Heel M IUCrJ. 2017 Aug 31;4(Pt 5):678-694. doi: 10.1107/S2052252517010922. eCollection, 2017 Sep 1. PMID:28989723<ref>PMID:28989723</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5m3l" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
== References ==
<references/>
__TOC__
</SX>
[[Category: Large Structures]]
[[Category: Lumbricus terrestris]]
[[Category: Afanasyev P]]
[[Category: Alewijnse B]]
[[Category: De Carlo S]]
[[Category: Linnemayr-Seer C]]
[[Category: Matadeen R]]
[[Category: Pannu NS]]
[[Category: Portugal RV]]
[[Category: Ravelli RBG]]
[[Category: Schatz M]]
[[Category: Van Heel M]]
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