9ZC4 | pdb_00009zc4

Cryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk

• PDB DOI: https://doi.org/10.2210/pdb9ZC4/pdb
• EM Map EMD-74030: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Leishmania tarentolae
• Mutation(s): No 


• Deposited: 2025-11-22 Released: 2026-10-07 
• Deposition Author(s): Liao, Y.T., Chao, L.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Conserved and divergent mitochondrial assemblies in kinetoplastid parasites.

Solayman, M., Liao, Y.T., Calvo, S.E., Vacas, A.F., Papanastasiou, M., Rivera, K.D., Mani, D.R., Boyle, B.W., Deng, F.G., Udeshi, N.D., Mootha, V.K., Aphasizheva, I., Chao, L.H., Aphasizhev, R.

(2026) Mol Cell 86: 4043

• PubMed: 42822418 
• DOI: https://doi.org/10.1016/j.molcel.2026.08.031
• Primary Citation Related Structures: 
  9Z9K, 9ZAK, 9ZB4, 9ZC4, 9ZC5


• PubMed Abstract: 
  

  The mitochondrial proteomes of Leishmania tarentolae and Trypanosoma brucei contain ∼1,700 proteins, most of which lack homologs in higher eukaryotes. Here, we integrate complexome profiling and cryo-electron microscopy to define conserved and lineage-specific macromolecular assemblies that support mitochondrial functions in these kinetoplastid protozoa. Comparative analyses reveal species- and life-stage-dependent differences in the abundance and composition of respiratory, metabolic, RNA processing, and other complexes, refining and expanding current annotations. Structures of L. tarentolae respiratory complex III ₂ (CIII ₂ ), complex IV ₂ (CIV ₂ ), and complex V (CV) identify nine previously unrecognized nuclear-encoded subunits and resolve five mitochondrially encoded proteins, including products of pan-edited mRNAs. These reconstructions uncover architectural innovations: a subunit 8 of ubiquinol cytochrome-c reductase (QCR8) N-terminal extension that plugs the vestigial mitochondrial processing peptidase (MPP)α/β cavity in CIII ₂ , a CIV ₂ dimer stabilized by an extensive clade-restricted interface, and a CV dimer containing the mitochondrially encoded ATP6 subunit. Together, our findings reveal how kinetoplastids assemble specialized mitochondrial machinery while incorporating diverged components into core modules shared across eukaryotes.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 94.47 kDa 
• Atom Count: 5,949 
• Modeled Residue Count: 756 
• Deposited Residue Count: 842 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ATP synthase subunit 8	A [auth J]	83	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KSU1 (Leishmania tarentolae) Explore A0A640KSU1  Go to UniProtKB:  A0A640KSU1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ATP synthase subunit ATPTB4	B [auth L]	137	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KVH9 (Leishmania tarentolae) Explore A0A640KVH9  Go to UniProtKB:  A0A640KVH9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3	C [auth R]	258	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A640KG49 (Leishmania tarentolae) Explore A0A640KG49  Go to UniProtKB:  A0A640KG49

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ATP synthase subunit d	D [auth K]	364	Leishmania tarentolae	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Liao, Y.T., Chao, L.

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

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release
  
• Version 1.1: 2026-10-14
  Changes: Data collection, Database references