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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BA [auth B]220Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFC7 (Escherichia coli (strain K12))
Explore P0AFC7 
Go to UniProtKB:  P0AFC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFC7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence 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))
Explore P33599 
Go to UniProtKB:  P33599
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33599
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence 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
Find proteins for P0AFD1 (Escherichia coli (strain K12))
Explore P0AFD1 
Go to UniProtKB:  P0AFD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFD1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence 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
Find proteins for P31979 (Escherichia coli (strain K12))
Explore P31979 
Go to UniProtKB:  P31979
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31979
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence 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
Find proteins for P33602 (Escherichia coli (strain K12))
Explore P33602 
Go to UniProtKB:  P33602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33602
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence 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
Find proteins for P0AFD6 (Escherichia coli (strain K12))
Explore P0AFD6 
Go to UniProtKB:  P0AFD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFD6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KG [auth K]100Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFE4 (Escherichia coli (strain K12))
Explore P0AFE4 
Go to UniProtKB:  P0AFE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JH [auth J]184Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFE0 (Escherichia coli (strain K12))
Explore P0AFE0 
Go to UniProtKB:  P0AFE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFE0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AI [auth A]147Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFC3 (Escherichia coli (strain K12))
Explore P0AFC3 
Go to UniProtKB:  P0AFC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFC3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HJ [auth H]325Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFD4 (Escherichia coli (strain K12))
Explore P0AFD4 
Go to UniProtKB:  P0AFD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFD4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit MK [auth M]509Escherichia coli BMutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AFE8 (Escherichia coli (strain K12))
Explore P0AFE8 
Go to UniProtKB:  P0AFE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFE8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit L613Escherichia 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
Find proteins for P33607 (Escherichia coli (strain K12))
Explore P33607 
Go to UniProtKB:  P33607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33607
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for P0AFF0 (Escherichia coli (strain K12))
Explore P0AFF0 
Go to UniProtKB:  P0AFF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFF0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
Q [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
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-UHFFFAOYSA-N
FES
Query on FES

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

Download Ideal Coordinates CCD File 
V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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

View Full Validation Report



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