7NYR

Respiratory complex I from Escherichia coli - conformation 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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: 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 ...

    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: 

    Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BA [auth B]220Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP0AFC7
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DB [auth D]596Escherichia coli BMutation(s): 0 
EC: 7.1.1.2 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P33599 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit EC [auth E]166Escherichia coli BMutation(s): 0 
EC: 7.1.1.2 (PDB Primary Data), 7.1.1 (UniProt)
UniProt
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UniProt GroupP0AFD1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FD [auth F]445Escherichia coli BMutation(s): 0 
EC: 7.1.1.2 (PDB Primary Data), 7.1.1 (UniProt)
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit GE [auth G]908Escherichia coli BMutation(s): 0 
EC: 7.1.1.2 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]180Escherichia coli BMutation(s): 0 
EC: 7.1.1.2 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KG [auth K]100Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JH [auth J]184Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 9
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NADH-quinone oxidoreductase subunit AI [auth A]147Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HJ [auth H]325Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit MK [auth M]509Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit LL613Escherichia 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), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence 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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
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Q [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
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N [auth B],
P [auth F],
S [auth G],
T [auth G],
U [auth G],
N [auth B],
P [auth F],
S [auth G],
T [auth G],
U [auth G],
W [auth I],
X [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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O [auth E],
R [auth G]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX		A [auth B]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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