9ZFV | pdb_00009zfv

Mitochondrial MDH and OSCP in the peripheral stalk of ATP synthase in Acanthamoeba castellanii

• PDB DOI: https://doi.org/10.2210/pdb9ZFV/pdb
• EM Map EMD-74155: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Acanthamoeba castellanii
• Mutation(s): No 


• Deposited: 2025-12-02 Released: 2026-10-14 
• Deposition Author(s): Fry, M.Y., Luce, B.E., Stefely, J.A., Samuelson, J., Mootha, V.K., Chao, L.H.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS.

Fry, M.Y., Luce, B.E., Stefely, J.A., Chen, M.Z., Deng, F.G., Issa, T.M., Calvo, S.E., Samuelson, J., Mootha, V.K., Chao, L.H.

(2026) Cell 189: 6307-6324.e7

• PubMed: 42822427 
• DOI: https://doi.org/10.1016/j.cell.2026.08.057
• Primary Citation Related Structures: 
  9ZFR, 9ZFS, 9ZFT, 9ZFU, 9ZFV, 9ZFW, 9ZFX


• PubMed Abstract: 
  

  Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.

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Organizational Affiliation: 
• Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118, USA.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118, USA.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 157.25 kDa 
• Atom Count: 7,698 
• Modeled Residue Count: 1,001 
• Deposited Residue Count: 1,431 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
malate dehydrogenase	A, B	454	Acanthamoeba castellanii	Mutation(s): 0  EC: 1.1.1.37
UniProt
Find proteins for L8HFT9 (Acanthamoeba castellanii (strain ATCC 30010 / Neff)) Explore L8HFT9  Go to UniProtKB:  L8HFT9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ATP synthase subunit oscp	C [auth G]	431	Acanthamoeba castellanii	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACANB14707	D [auth C]	92	Acanthamoeba castellanii	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Fry, M.Y., Luce, B.E., Stefely, J.A., Samuelson, J., Mootha, V.K., Chao, L.H.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release