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 9ZB4 | pdb_00009zb4

Cryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) membrane region


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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

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This is version 1.1 of the entry. See complete history. 

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

  • 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.


  • Organizational Affiliation: 
    • Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.

Macromolecule Content 

  • Total Structure Weight: 586.09 kDa 
  • Atom Count: 41,236 
  • Modeled Residue Count: 5,124 
  • Deposited Residue Count: 5,124 
  • Unique protein chains: 15

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LtaP27_632926_633111, LtATPEG4A [auth o],
VA [auth O]
55Leishmania tarentolaeMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit c-176Leishmania tarentolaeMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase 6L [auth l],
Y [auth L]
231Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q33561 (Leishmania tarentolae)
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UniProt GroupQ33561
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit i/jM [auth b],
Z [auth B]
102Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640K7R8 (Leishmania tarentolae)
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UniProt GroupA0A640K7R8
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ATPTB1N [auth d],
SA [auth D]
384Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KLU7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ATPTB6AA [auth H],
O [auth h]
163Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KJ33 (Leishmania tarentolae)
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UniProt GroupA0A640KJ33
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit gBA [auth I],
P [auth i]
127Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KX01 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit fCA [auth E],
Q [auth e]
123Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KHR7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit 8DA [auth J],
R [auth j]
66Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KSU1 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit bEA [auth K],
S [auth k]
75Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KSG2 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit eFA [auth M],
T [auth m]
59Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KHE9 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit kTA [auth G],
U [auth g]
104Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KJQ9 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ATPTB12GA [auth A],
V [auth a]
99Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KES0 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ATPTB11HA [auth F],
W [auth f]
136Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KHW7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ATPEG3UA [auth N],
X [auth n]
78Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KG00 (Leishmania tarentolae)
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

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