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 9Z9K | pdb_00009z9k

Cryo-EM structure of Leishmania tarentolae respiratory complex III (cytochrome bc1 complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: 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: 587.07 kDa 
  • Atom Count: 41,308 
  • Modeled Residue Count: 5,116 
  • Deposited Residue Count: 5,116 
  • Unique protein chains: 12

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial processing peptidase alpha subunit, putativeA,
L [auth a]
479Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KGT7 (Leishmania tarentolae)
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UniProt GroupA0A640KGT7
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial processing peptide beta subunit, putativeB,
M [auth b]
490Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KTP0 (Leishmania tarentolae)
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UniProt GroupA0A640KTP0
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 14 kDa proteinC,
N [auth c]
191Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KSC9 (Leishmania tarentolae)
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UniProt GroupA0A640KSC9
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bD,
O [auth d]
371Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for P14548 (Leishmania tarentolae)
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UniProt GroupP14548
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial, putativeE,
P [auth e]
258Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KA58 (Leishmania tarentolae)
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UniProt GroupA0A640KA58
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
LtaP17.1410, Hypothetical protein, conservedF,
Q [auth f]
67Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KF59 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
LtaP32.3800, Hypothetical protein, conservedG,
R [auth g]
147Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KPN1 (Leishmania tarentolae)
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UniProt GroupA0A640KPN1
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Rieske iron-sulfur protein, putativeH,
S [auth h]
279Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KYQ2 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
LtaP35.0250, Hypothetical protein, conservedI,
T [auth i]
107Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KRZ1 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome-c reductase-like proteinJ,
U [auth j]
70Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KNT3 (Leishmania tarentolae)
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UniProt GroupA0A640KNT3
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
LtaP27.0110, Hypothetical protein, conservedK,
V [auth k]
75Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KKU7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned helixW [auth L],
X [auth l]
24Leishmania tarentolaeMutation(s): 0 
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.7.0

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