Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation

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Data availability
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Abstract

Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against trans-membrane potential. Complex I from Escherichia coli is among the best functionally characterized complexes, but its structure remains unknown, hindering further mechanistic studies to understand the enzyme coupling mechanism. Here we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active E. coli complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data we suggest a new simple hypothetical coupling mechanism for the molecular machine.

Data availability

Cryo-EM density maps and atomic models are deposited into the PDB and EMDB databases with the following accession codes: cytoplasmic domain (PDB ID: 7NZ1, EMD-12661), membrane domain (PDB ID: 7NYH, EMD-12652), entire complex conformation 1 (PDB ID: 7NYR, EMD-12653), conformation 2 (PDB ID: 7NYU,EMD-12654), conformation 3 (PDB ID: 7NYV, EMD-12655).

The following data sets were generated

1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm
Electron Microscopy Data Bank ID EMD-12661.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-12661
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - focused refinement of membrane arm
Electron Microscopy Data Bank ID EMD-12652.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-12652
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 1
Electron Microscopy Data Bank ID EMD-12653.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-12653
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 2
Electron Microscopy Data Bank ID EMD-12654.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-12654
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 3
Electron Microscopy Data Bank ID EMD-12655.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-12655
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm
RCSB Protein Data Bank ID 7NZ1.

https://www.rcsb.org/structure/7NZ1
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - focused refinement of membrane arm
RCSB Protein Data Bank ID 7NYH.

https://www.rcsb.org/structure/7NYH
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 1
RCSB Protein Data Bank ID 7NYR.

https://www.rcsb.org/structure/7NYR
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 2
RCSB Protein Data Bank ID 7NYU.

https://www.rcsb.org/structure/7NYU
1. Kolata P
2. Efremov RG
(2021) Respiratory complex I from Escherichia coli - conformation 3
RCSB Protein Data Bank ID 7NYV.

https://www.rcsb.org/structure/7NYV

The following previously published data sets were used

(2013) Crystal structure of the entire respiratory complex I from Thermus thermophilus
RCSB Protein Data Bank ID 4HEA.

https://www.rcsb.org/structure/4HEA
1. Efremov RG
2. Sazanov LA
(2011) Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution
RCSB Protein Data Bank ID 3RKO.

https://www.rcsb.org/structure/3RKO

Article and author information

Author details

Piotr Kolata

VIB Center for Structural Biology, VUB Structural Biology Brussels, VIB-VUB, Brussels, Belgium

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9484-5025
Rouslan G Efremov

VIB Center for Structural Biology, VUB Structural Biology Brussels, VIB-VUB, Brussels, Belgium

For correspondence
rouslan.efremov@vub.vib.be

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7516-8658

Funding

Fonds Wetenschappelijk Onderzoek (G0H5916N)

Rouslan G Efremov

Fonds Wetenschappelijk Onderzoek (G.0266.15N)

Rouslan G Efremov

H2020 European Research Council (726436)

Rouslan G Efremov

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.