7NYU

Respiratory complex I from Escherichia coli - conformation 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

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

Kolata, P.Efremov, R.G.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.68710
  • Primary Citation of Related Structures:  
    7NYH, 7NYR, 7NYU, 7NYV, 7NZ1

  • PubMed Abstract: 

    Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from Escherichia coli is among the best functionally characterized complexes, but its structure remains unknown, hindering further 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.


  • Organizational Affiliation

    Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit A147Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP0AFC3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit B220Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP0AFC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DC [auth D]596Escherichia coli BMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP33599
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit ED [auth E]166Escherichia coli BMutation(s): 0 
EC: 7.1.1.2
UniProt
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UniProt GroupP0AFD1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FE [auth F]445Escherichia coli BMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit GF [auth G]908Escherichia coli BMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IH [auth I]180Escherichia coli BMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JI [auth J]184Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KJ [auth K]100Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit LK [auth L]613Escherichia coli BMutation(s): 0 
EC: 1.6.5.11 (PDB Primary Data), 1.6.5.3 (PDB Primary Data), 1.6.99.5 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit ML [auth M]509Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NM [auth N]485Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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P [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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N [auth B]
Q [auth F]
S [auth G]
T [auth G]
U [auth G]
N [auth B],
Q [auth F],
S [auth G],
T [auth G],
U [auth G],
W [auth I],
X [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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O [auth E],
R [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA

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V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONPHENIX1.18.2
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Belgium00281ROEF

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release