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== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.


RELION: implementation of a Bayesian approach to cryo-EM structure determination.,Scheres SH J Struct Biol. 2012 Dec;180(3):519-30. doi: 10.1016/j.jsb.2012.09.006. Epub 2012 , Sep 19. PMID:23000701<ref>PMID:23000701</ref>
Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog.,Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguene VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P Commun Biol. 2022 Apr 13;5(1):355. doi: 10.1038/s42003-022-03306-y. PMID:35418619<ref>PMID:35418619</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

Revision as of 15:59, 4 May 2022

Structure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopyStructure of ExbB pentamer from Serratia marcescens by single particle cryo electron microscopy

Structural highlights

6ye4 is a 5 chain structure with sequence from "bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:exbB, FG174_21755, PWN146_03792 ("Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbBSm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbBSm and HasB. We determined the cryo-EM structures of ExbBSm and of the ExbB-ExbDSm complex from S. marcescens. ExbBSm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbBSm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbBSm and ExbBEc, essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.

Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog.,Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguene VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P Commun Biol. 2022 Apr 13;5(1):355. doi: 10.1038/s42003-022-03306-y. PMID:35418619[1]

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

See Also

References

  1. ↑ Biou V, Adaixo RJD, Chami M, Coureux PD, Laurent B, Enguene VYN, de Amorim GC, Izadi-Pruneyre N, Malosse C, Chamot-Rooke J, Stahlberg H, Delepelaire P. Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog. Commun Biol. 2022 Apr 13;5(1):355. doi: 10.1038/s42003-022-03306-y. PMID:35418619 doi:http://dx.doi.org/10.1038/s42003-022-03306-y

6ye4, resolution 3.20Å

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