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- PDB-9zc5: Cryo-EM structure of Leishmania tarentolae respiratory complex V ... -

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Basic information

Entry
Database: PDB / ID: 9zc5
TitleCryo-EM structure of Leishmania tarentolae respiratory complex V (ATP synthase) Fo monomer membrane region
Components
  • (Mitochondrial ATP synthase subunit ...) x 13
  • ATPase 6
  • LtATPEG4, LtaP27:632926-633111
KeywordsELECTRON TRANSPORT / Electron transport chain / respiratory complex / ATP synthase / mitochondria
Function / homology
Function and homology information


Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Uncharacterized protein / Letm1 RBD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / ATPase 6
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 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

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Assembly

Deposited unit
A: Mitochondrial ATP synthase subunit ATPTB12
B: Mitochondrial ATP synthase subunit i/j
C: Mitochondrial ATP synthase subunit c-1
D: Mitochondrial ATP synthase subunit ATPTB1
E: Mitochondrial ATP synthase subunit f
F: Mitochondrial ATP synthase subunit ATPTB11
G: Mitochondrial ATP synthase subunit k
H: Mitochondrial ATP synthase subunit ATPTB6
I: Mitochondrial ATP synthase subunit g
J: Mitochondrial ATP synthase subunit 8
K: Mitochondrial ATP synthase subunit b
L: ATPase 6
M: Mitochondrial ATP synthase subunit e
N: Mitochondrial ATP synthase subunit ATPEG3
O: LtATPEG4, LtaP27:632926-633111
P: Mitochondrial ATP synthase subunit c-1
Q: Mitochondrial ATP synthase subunit c-1
R: Mitochondrial ATP synthase subunit c-1
S: Mitochondrial ATP synthase subunit c-1
T: Mitochondrial ATP synthase subunit c-1
U: Mitochondrial ATP synthase subunit c-1
V: Mitochondrial ATP synthase subunit c-1
W: Mitochondrial ATP synthase subunit c-1
X: Mitochondrial ATP synthase subunit c-1


Theoretical massNumber of molelcules
Total (without water)293,04524
Polymers293,04524
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

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Mitochondrial ATP synthase subunit ... , 13 types, 22 molecules ABCPQRSTUVWXDEFGHIJKMN

#1: Protein Mitochondrial ATP synthase subunit ATPTB12


Mass: 11454.896 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: A0A640KES0
#2: Protein Mitochondrial ATP synthase subunit i/j


Mass: 12293.158 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: A0A640K7R8
#3: Protein
Mitochondrial ATP synthase subunit c-1


Mass: 7854.518 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
#4: Protein Mitochondrial ATP synthase subunit ATPTB1


Mass: 45347.246 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: A0A640KLU7
#5: Protein Mitochondrial ATP synthase subunit f


Mass: 14321.474 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: A0A640KHR7
#6: Protein Mitochondrial ATP synthase subunit ATPTB11


Mass: 15722.698 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: A0A640KHW7
#7: Protein Mitochondrial ATP synthase subunit k


Mass: 12026.902 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: A0A640KJQ9
#8: Protein Mitochondrial ATP synthase subunit ATPTB6


Mass: 19162.000 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: A0A640KJ33
#9: Protein Mitochondrial ATP synthase subunit g


Mass: 14702.046 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: A0A640KX01
#10: Protein Mitochondrial ATP synthase subunit 8


Mass: 8299.618 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
#11: Protein Mitochondrial ATP synthase subunit b


Mass: 9043.121 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: A0A640KSG2
#13: Protein Mitochondrial ATP synthase subunit e


Mass: 6960.852 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: A0A640KHE9
#14: Protein Mitochondrial ATP synthase subunit ATPEG3


Mass: 10147.562 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: A0A640KG00

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Protein , 2 types, 2 molecules LO

#12: Protein ATPase 6 / MURF4 protein


Mass: 28261.975 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: Q33561
#15: Protein LtATPEG4, LtaP27:632926-633111


Mass: 6756.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)

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Details

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: Fo monomer membrane region of Leishmania tarentolae respiratory complex V (ATP synthase)
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: #13, #15, #3, #12, #2, #4, #8-#9, #5, #10-#11, #7, #1, #6, #14
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
7Coot0.9.6model fitting
8ISOLDE1.12model fitting
11cryoSPARC4.7final Euler assignment
13cryoSPARC4.73D reconstruction
20PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8358 / Symmetry type: POINT
Atomic model buildingDetails: Built de novo using ModelAngelo (v1.014), guided by the cryo-EM density map
Source name: Other / Type: in silico model
RefinementHighest resolution: 3.62 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221184
ELECTRON MICROSCOPYf_angle_d0.46128672
ELECTRON MICROSCOPYf_dihedral_angle_d12.4117541
ELECTRON MICROSCOPYf_chiral_restr0.0363078
ELECTRON MICROSCOPYf_plane_restr0.0043593

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