9Q8I | pdb_00009q8i

Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.

Wohlwend, D.Seifermann, T.Gnandt, E.Vranas, M.Gerhardt, S.Friedrich, T.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.10.016
  • Primary Citation of Related Structures:  
    9HE5, 9HEG, 9HEM, 9HEN, 9Q8I

  • PubMed Abstract: 

    Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.


  • Organizational Affiliation
    • Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit A147Escherichia coliMutation(s): 0 
Gene Names: nuoAb2288JW2283
EC: 7.1.1
UniProt
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UniProt GroupP0AFC3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit B220Escherichia coliMutation(s): 0 
Gene Names: nuoBb2287JW5875
EC: 7.1.1
UniProt
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UniProt GroupP0AFC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/D596Escherichia coliMutation(s): 0 
Gene Names: nuoCnuoCDnuoDb2286JW5375
EC: 7.1.1
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit ED [auth E]166Escherichia coliMutation(s): 2 
Gene Names: nuoEb2285JW2280
EC: 7.1.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FE [auth F]461Escherichia coliMutation(s): 0 
Gene Names: nuoFb2284JW2279
EC: 7.1.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit GF [auth G]908Escherichia coliMutation(s): 0 
Gene Names: nuoGb2283JW2278
EC: 7.1.1
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coliMutation(s): 0 
Gene Names: nuoHb2282JW2277
EC: 7.1.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IH [auth I]180Escherichia coliMutation(s): 0 
Gene Names: nuoIb2281JW2276
EC: 7.1.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JI [auth J]184Escherichia coliMutation(s): 0 
Gene Names: nuoJb2280JW2275
EC: 7.1.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KJ [auth K]100Escherichia coliMutation(s): 0 
Gene Names: nuoKb2279JW2274
EC: 7.1.1
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit LK [auth L]613Escherichia coliMutation(s): 0 
Gene Names: nuoLb2278JW2273
EC: 7.1.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit ML [auth M]509Escherichia coliMutation(s): 0 
Gene Names: nuoMb2277JW2272
EC: 7.1.1
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NM [auth N]485Escherichia coliMutation(s): 0 
Gene Names: nuoNb2276JW2271
EC: 7.1.1
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth L]
CA [auth L]
DA [auth L]
EA [auth L]
AA [auth J],
BA [auth L],
CA [auth L],
DA [auth L],
EA [auth L],
FA [auth M],
GA [auth M],
HA [auth N],
IA [auth N],
N [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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R [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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O [auth B]
Q [auth F]
S [auth G]
T [auth G]
U [auth G]
O [auth B],
Q [auth F],
S [auth G],
T [auth G],
U [auth G],
Y [auth I],
Z [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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

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W [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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JA [auth N],
X [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONUCSF ChimeraX1.7.1
RECONSTRUCTIONUCSF ChimeraX1.7.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFR 1140/11-2
German Research Foundation (DFG)Germany278002225

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references