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 9ZAK | pdb_00009zak

Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 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: 756.02 kDa 
  • Atom Count: 53,313 
  • Modeled Residue Count: 6,448 
  • Deposited Residue Count: 6,450 
  • Unique protein chains: 17

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P27 proteinA,
R [auth a]
223Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KL16 (Leishmania tarentolae)
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UniProt GroupA0A640KL16
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit V, putativeB,
S [auth b]
179Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KIZ0 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2C,
T [auth c]
210Leishmania tarentolaeMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P14545 (Leishmania tarentolae)
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UniProt GroupP14545
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome C oxidase subunit VI, putativeD,
U [auth d]
157Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KLX8 (Leishmania tarentolae)
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UniProt GroupA0A640KLX8
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein, conserved, LtaP04.0630E,
V [auth e]
200Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640K7Y4 (Leishmania tarentolae)
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UniProt GroupA0A640K7Y4
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase VIII, putativeF,
W [auth f]
127Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KN71 (Leishmania tarentolae)
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UniProt GroupA0A640KN71
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein, conserved, LtaP09.0030G,
X [auth g]
107Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640K9E6 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase VII, putativeH,
Y [auth h]
165Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KP32 (Leishmania tarentolae)
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UniProt GroupA0A640KP32
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome-c oxidaseI [auth K],
Z [auth k]
202Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KV26 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 10AA [auth l],
J [auth L]
95Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KG51 (Leishmania tarentolae)
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UniProt GroupA0A640KG51
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit IBA [auth m],
K [auth M]
110Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KXE6 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1CA [auth n],
L [auth N]
549Leishmania tarentolaeMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P14544 (Leishmania tarentolae)
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UniProt GroupP14544
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3DA [auth o],
M [auth O]
287Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q34935 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein, conserved, LtaP33.2260EA [auth p],
N [auth P]
93Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KQD4 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein, conserved, LtaP36.1760FA [auth q],
O [auth Q]
82Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KUH3 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit ivGA [auth r],
P [auth R]
311Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KB61 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase assembly factor like proteinHA [auth s],
Q [auth S]
128Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640K8B8 (Leishmania tarentolae)
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 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