9PXK | pdb_00009pxk

CryoEM structure of Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PXK

This is version 1.1 of the entry. See complete history

Literature

Quinone-transporting filaments expand bioenergetic capacity in Gram-positive Bacillota.

Kropp, A.Asadollahi, K.Stapleton, J.A.Simsive, L.Leung, P.M.Darnell, R.L.Barlow, C.K.Hartmann, B.G.Yates, N.D.J.Lumbantobing, T.Fox, D.R.Greening, C.Zdorevskyi, O.Sharma, V.Blaza, J.N.Parkin, A.Grinter, R.

(2026) Nat Microbiol 11: 2543-2561

  • DOI: https://doi.org/10.1038/s41564-026-02450-z
  • Primary Citation Related Structures: 
    9PXK, 9PXL, 9PXM

  • PubMed Abstract: 

    Cellular respiration depends on transferring electrons to hydrophobic quinones in membrane bilayers, meaning bioenergetic capacity is constrained by available membrane surface area. While Gram-negative bacteria expand this capacity through internal membrane invaginations and eukaryotes use membrane-bound organelles, whether Gram-positive bacteria have alternative capacity-generating mechanisms is unknown. Here we show that Bacillus subtilis forms a quinone-transporting pseudomembrane composed of filaments of the NADH dehydrogenase Ndh and the quinone-transporting protein Ncp. Cryo-EM, lipidomics and molecular dynamics reveal that Ndh and Ncp co-assemble with lipids into a 4:4 stoichiometric complex with a solvent-excluded hydrophobic lumen containing phospholipids, which sequesters quinones. These complexes further assemble into filaments, linking chambers into a continuous conduit that amplifies quinone reduction. Phylogenetic analysis suggests that this capacity is widespread in Bacillota. Quinone-transporting filaments thus reveal a strategy to expand the quinone pool and bioenergetic capacity while occupying minimal membrane space.


  • Organizational Affiliation
    • Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 254.32 kDa 
  • Atom Count: 16,084 
  • Modeled Residue Count: 2,044 
  • Deposited Residue Count: 2,272 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH dehydrogenase-like protein YjlDA [auth C],
F [auth A],
G [auth B],
H [auth D]
392Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yjlDBSU12290
EC: 1.6.99
UniProt
Find proteins for P80861 (Bacillus subtilis (strain 168))
Explore P80861 
Go to UniProtKB:  P80861
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80861
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NDH-2 membrane coupling proteinB [auth E],
C [auth F],
D [auth G],
E [auth H]
176Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yjlCBSU12280
UniProt
Find proteins for O34633 (Bacillus subtilis (strain 168))
Explore O34633 
Go to UniProtKB:  O34633
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34633
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
I [auth C],
L [auth A],
O [auth B],
R [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MQ8
(Subject of Investigation/LOI)

Query on MQ8



Download:Ideal Coordinates CCD File
J [auth C],
M [auth A],
P [auth B],
S [auth D]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
NAI
(Subject of Investigation/LOI)

Query on NAI



Download:Ideal Coordinates CCD File
K [auth C],
N [auth A],
Q [auth B],
T [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP230103080

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references