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- PDB-9zc4: Cryo-EM structure of Leishmania tarentolae respiratory complex V ... -

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Basic information

Entry
Database: PDB / ID: 9zc4
TitleCryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
Components
  • LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3
  • mitochondrial ATP synthase subunit 8
  • mitochondrial ATP synthase subunit ATPTB4
  • mitochondrial ATP synthase subunit d
KeywordsELECTRON TRANSPORT / Electron transport chain / respiratory complex / ATP synthase / mitochondria
Function / homologyUncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsLiao, Y.T. / Chao, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2026
Title: Conserved and divergent mitochondrial assemblies in kinetoplastid parasites
Authors: Solayman, M. / Liao, Y.T. / Calvo, S.E. / Vacas, A.F. / Papanastasiou, M. / Rivera, K.D. / Mani, D. / Boyle, B.W. / Deng, F.G. / Betsinger, C.N. / Carr, S.A. / Chen, M.Z. / Duraisingh, M.T. ...Authors: Solayman, M. / Liao, Y.T. / Calvo, S.E. / Vacas, A.F. / Papanastasiou, M. / Rivera, K.D. / Mani, D. / Boyle, B.W. / Deng, F.G. / Betsinger, C.N. / Carr, S.A. / Chen, M.Z. / Duraisingh, M.T. / Fry, M.Y. / Goyal, M. / Issa, T.M. / Kim, M. / Lian, C.G. / Luce, B.E. / Mian, S.Y. / Nguyen, K. / Paul, A.S. / Samuelson, J. / Stefely, J.A. / Udeshi, N.D. / Mootha, V.K. / Aphasizheva, I. / Chao, L.H. / Aphasizhev, R.
History
DepositionNov 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: mitochondrial ATP synthase subunit 8
L: mitochondrial ATP synthase subunit ATPTB4
R: LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3
K: mitochondrial ATP synthase subunit d


Theoretical massNumber of molelcules
Total (without water)94,4724
Polymers94,4724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein mitochondrial ATP synthase subunit 8


Mass: 10145.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KSU1
#2: Protein mitochondrial ATP synthase subunit ATPTB4


Mass: 15343.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KVH9
#3: Protein LtaP11.1000, chain R, 92-349. mitochondrial ATP synthase subunit ATPTB3


Mass: 26703.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KG49
#4: Protein mitochondrial ATP synthase subunit d


Mass: 42279.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 1-29, 169-184, and 324-364 are not modeled due to the absence of density, resulting in breaks between residues 168-185
Source: (natural) Leishmania tarentolae (eukaryote)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Leishmania tarentolae respiratory complex V (ATP synthase) peripheral stalk
Type: COMPLEX
Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, ...Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, followed by centrifuging at 14,000 x g for 10 min. The supernatant was filtered prior to grid preparation.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Buffer solutionpH: 7.9
Details: 50 mM HEPES pH 7.9, 300 mM NaCl, 4 mM MgCl2, 20 uM CaCl2, 0.1 mM Dithiothreitol, and 0.5% n-dodecyl-beta-D-maltoside
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
4cryoSPARC4.7CTF correction
7UCSF ChimeraX1.6model fitting
8Coot0.9.6model fitting
9ISOLDE1.12model fitting
14cryoSPARC4.73D reconstruction
21PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8358 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.95 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026059
ELECTRON MICROSCOPYf_angle_d0.4968189
ELECTRON MICROSCOPYf_dihedral_angle_d11.1122279
ELECTRON MICROSCOPYf_chiral_restr0.034915
ELECTRON MICROSCOPYf_plane_restr0.0041047

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