9TAO | pdb_00009tao

Local refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9TAO

This is version 1.1 of the entry. See complete history

Literature

A carboxylate switch point controls long-range energy transduction in respiratory Complex I.

Beghiah, A.Saura, P.Kovalova, T.Hoeser, F.Friedrich, T.Kaila, V.R.I.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-74767-6
  • Primary Citation Related Structures: 
    9TAJ, 9TAK, 9TAL, 9TAM, 9TAN, 9TAO

  • PubMed Abstract: 

    Complex I is a highly intricate membrane-bound protein complex that powers the cellular energy metabolism by a long-range ( > 300 Å) proton-coupled electron transfer (PCET) reaction. Here, we investigate the highly debated coupling mechanism of Complex I by probing the charge transfer reaction along its functionally central carboxylate pathway (E-channel). By combining biophysical and site-directed mutagenesis experiments with high-resolution (2.6-2.8 Å) cryo-electron microscopy (cryo-EM) and multiscale simulations, we identify a conserved carboxylate switch point (D79 NuoA ) that mediates proton transfer by establishing a kinetic gate and couples the redox chemistry to proton pumping. We find that mutation of the identified site, as found in patients suffering from severe neurodegenerative disorders, drastically perturbs the charge transfer mechanism, and results in a 20% PCET activity. Our combined findings illustrate mechanistic principles of molecular gates underlying long-range charge transfer reactions, and show how disease mutations perturb the function of conserved switch points in energy transduction.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 273.29 kDa 
  • Atom Count: 18,764 
  • Modeled Residue Count: 2,281 
  • Deposited Residue Count: 2,363 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HA [auth H]325Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoHb2282JW2277
EC: 7.1.1
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KB [auth K]100Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoKb2279JW2274
EC: 7.1.1
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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit LC [auth L]613Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoLb2278JW2273
EC: 7.1.1
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:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AD [auth A]147Escherichia coli BW25113Mutation(s): 1 
Gene Names: nuoAb2288JW2283
EC: 7.1.1
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:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JE [auth J]184Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoJb2280JW2275
EC: 7.1.1
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:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit MF [auth M]509Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoMb2277JW2272
EC: 7.1.1
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:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NG [auth N]485Escherichia coli BW25113Mutation(s): 0 
Gene Names: nuoNb2276JW2271
EC: 7.1.1
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
CDL

Query on CDL



Download:Ideal Coordinates CCD File
N [auth A]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
H
I [auth H]
K [auth L]
L
M [auth L]
H,
I [auth H],
K [auth L],
L,
M [auth L],
O [auth A],
P [auth J],
S [auth M],
V [auth N],
W [auth N],
X [auth N],
Y [auth N]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
UQ8
(Subject of Investigation/LOI)

Query on UQ8



Download:Ideal Coordinates CCD File
AA [auth N],
Z [auth N]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
7PH

Query on 7PH



Download:Ideal Coordinates CCD File
J [auth H],
Q [auth J],
R [auth J],
T [auth M],
U [auth M]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden2024.0220
Swedish Research CouncilSweden2020-04081

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references