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- PDB-9zak: Cryo-EM structure of Leishmania tarentolae respiratory complex IV... -

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Basic information

Entry
Database: PDB / ID: 9zak
TitleCryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)
Components
  • (Cytochrome c oxidase ...) x 11
  • (Hypothetical protein, conserved, ...) x 4
  • Cytochrome-c oxidase
  • P27 protein
KeywordsELECTRON TRANSPORT / Electron transport chain / respiratory complex / cytochrome c oxidase / mitochondria
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / mitochondrial inner membrane / copper ion binding ...aerobic electron transport chain / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / membrane
Similarity search - Function
Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) ...Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / HEME-A / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome c oxidase subunit iv / Cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit V, putative / P27 protein / Cytochrome C oxidase subunit VI, putative ...COPPER (II) ION / HEME-A / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome c oxidase subunit iv / Cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit V, putative / P27 protein / Cytochrome C oxidase subunit VI, putative / Cytochrome c oxidase VIII, putative / Cytochrome c oxidase VII, putative / Uncharacterized protein / Uncharacterized protein / Cytochrome-c oxidase / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 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 19, 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
A: P27 protein
B: Cytochrome c oxidase subunit V, putative
C: Cytochrome c oxidase subunit 2
D: Cytochrome C oxidase subunit VI, putative
E: Hypothetical protein, conserved, LtaP04.0630
F: Cytochrome c oxidase VIII, putative
G: Hypothetical protein, conserved, LtaP09.0030
H: Cytochrome c oxidase VII, putative
K: Cytochrome-c oxidase
L: Cytochrome c oxidase subunit 10
M: Cytochrome c oxidase subunit I
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 3
P: Hypothetical protein, conserved, LtaP33.2260
Q: Hypothetical protein, conserved, LtaP36.1760
R: Cytochrome c oxidase subunit iv
S: Cytochrome c oxidase assembly factor like protein
a: P27 protein
b: Cytochrome c oxidase subunit V, putative
c: Cytochrome c oxidase subunit 2
d: Cytochrome C oxidase subunit VI, putative
e: Hypothetical protein, conserved, LtaP04.0630
f: Cytochrome c oxidase VIII, putative
g: Hypothetical protein, conserved, LtaP09.0030
h: Cytochrome c oxidase VII, putative
k: Cytochrome-c oxidase
l: Cytochrome c oxidase subunit 10
m: Cytochrome c oxidase subunit I
n: Cytochrome c oxidase subunit 1
o: Cytochrome c oxidase subunit 3
p: Hypothetical protein, conserved, LtaP33.2260
q: Hypothetical protein, conserved, LtaP36.1760
r: Cytochrome c oxidase subunit iv
s: Cytochrome c oxidase assembly factor like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)756,02540
Polymers752,48634
Non-polymers3,5386
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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Protein , 2 types, 4 molecules AaKk

#1: Protein P27 protein


Mass: 25912.838 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KL16
#9: Protein Cytochrome-c oxidase


Mass: 23705.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KV26

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Cytochrome c oxidase ... , 11 types, 22 molecules BbCcDdFfHhLlMmNnOoRrSs

#2: Protein Cytochrome c oxidase subunit V, putative


Mass: 20361.264 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KIZ0
#3: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 23988.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: P14545, cytochrome-c oxidase
#4: Protein Cytochrome C oxidase subunit VI, putative


Mass: 19310.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KLX8
#6: Protein Cytochrome c oxidase VIII, putative


Mass: 15495.813 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KN71
#8: Protein Cytochrome c oxidase VII, putative


Mass: 19136.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KP32
#10: Protein Cytochrome c oxidase subunit 10


Mass: 11616.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KG51
#11: Protein Cytochrome c oxidase subunit I


Mass: 12034.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KXE6
#12: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 63297.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: P14544, cytochrome-c oxidase
#13: Protein Cytochrome c oxidase subunit 3


Mass: 34184.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: Q34935
#16: Protein Cytochrome c oxidase subunit iv


Mass: 35969.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KB61
#17: Protein Cytochrome c oxidase assembly factor like protein


Mass: 15137.333 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640K8B8

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Hypothetical protein, conserved, ... , 4 types, 8 molecules EeGgPpQq

#5: Protein Hypothetical protein, conserved, LtaP04.0630


Mass: 23408.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640K7Y4
#7: Protein Hypothetical protein, conserved, LtaP09.0030


Mass: 12414.288 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640K9E6
#14: Protein Hypothetical protein, conserved, LtaP33.2260


Mass: 10566.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KQD4
#15: Protein Hypothetical protein, conserved, LtaP36.1760


Mass: 9704.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain) / References: UniProt: A0A640KUH3

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Non-polymers , 2 types, 6 molecules

#18: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#19: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6

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Details

Has ligand of interestN
Has protein modificationY

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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 mitochondria Complex IV / 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: #16, #9, #5, #2, #8, #17, #15, #4, #11, #7, #10, #1, #6, #14, #12-#13, #3
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
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
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5392 / 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: 3.21 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_d0.00355058
ELECTRON MICROSCOPYf_angle_d0.45974779
ELECTRON MICROSCOPYf_dihedral_angle_d11.2519509
ELECTRON MICROSCOPYf_chiral_restr0.0387820
ELECTRON MICROSCOPYf_plane_restr0.0049337

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