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- PDB-9z9k: Cryo-EM structure of Leishmania tarentolae respiratory complex II... -

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Basic information

Entry
Database: PDB / ID: 9z9k
TitleCryo-EM structure of Leishmania tarentolae respiratory complex III (cytochrome bc1 complex)
Components
  • (Mitochondrial processing ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial, putative
  • LtaP17.1410, Hypothetical protein, conserved
  • LtaP27.0110, Hypothetical protein, conserved
  • LtaP32.3800, Hypothetical protein, conserved
  • LtaP35.0250, Hypothetical protein, conserved
  • Rieske iron-sulfur protein, putative
  • Ubiquinol-cytochrome c reductase complex 14 kDa protein
  • Ubiquinol-cytochrome-c reductase-like protein
  • unassigned helix
KeywordsELECTRON TRANSPORT / cytochrome bc1 complex / respiratory complex / complex III / mitochondria
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : ...Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Rieske iron-sulphur protein / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c1, heme protein, mitochondrial, putative / Uncharacterized protein / Mitochondrial processing peptidase alpha subunit, putative / Uncharacterized protein / Ubiquinol-cytochrome-c reductase-like protein / Uncharacterized protein / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex 14 kDa protein / Mitochondrial processing peptide beta subunit, putative ...PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c1, heme protein, mitochondrial, putative / Uncharacterized protein / Mitochondrial processing peptidase alpha subunit, putative / Uncharacterized protein / Ubiquinol-cytochrome-c reductase-like protein / Uncharacterized protein / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex 14 kDa protein / Mitochondrial processing peptide beta subunit, putative / Rieske iron-sulfur protein, putative / Cytochrome b
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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 18, 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: Mitochondrial processing peptidase alpha subunit, putative
B: Mitochondrial processing peptide beta subunit, putative
C: Ubiquinol-cytochrome c reductase complex 14 kDa protein
D: Cytochrome b
E: Cytochrome c1, heme protein, mitochondrial, putative
F: LtaP17.1410, Hypothetical protein, conserved
G: LtaP32.3800, Hypothetical protein, conserved
H: Rieske iron-sulfur protein, putative
I: LtaP35.0250, Hypothetical protein, conserved
J: Ubiquinol-cytochrome-c reductase-like protein
K: LtaP27.0110, Hypothetical protein, conserved
a: Mitochondrial processing peptidase alpha subunit, putative
b: Mitochondrial processing peptide beta subunit, putative
c: Ubiquinol-cytochrome c reductase complex 14 kDa protein
d: Cytochrome b
e: Cytochrome c1, heme protein, mitochondrial, putative
f: LtaP17.1410, Hypothetical protein, conserved
g: LtaP32.3800, Hypothetical protein, conserved
h: Rieske iron-sulfur protein, putative
i: LtaP35.0250, Hypothetical protein, conserved
j: Ubiquinol-cytochrome-c reductase-like protein
k: LtaP27.0110, Hypothetical protein, conserved
L: unassigned helix
l: unassigned helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)587,06828
Polymers584,60224
Non-polymers2,4664
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 processing ... , 2 types, 4 molecules AaBb

#1: Protein Mitochondrial processing peptidase alpha subunit, putative


Mass: 52705.617 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: A0A640KGT7
#2: Protein Mitochondrial processing peptide beta subunit, putative


Mass: 54669.586 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: A0A640KTP0

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Protein , 9 types, 18 molecules CcDdEeFfGgHhIiJjKk

#3: Protein Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 23053.461 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: A0A640KSC9
#4: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 44579.051 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: P14548
#5: Protein Cytochrome c1, heme protein, mitochondrial, putative


Mass: 29907.707 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: A0A640KA58
#6: Protein LtaP17.1410, Hypothetical protein, conserved


Mass: 8021.193 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: A0A640KF59
#7: Protein LtaP32.3800, Hypothetical protein, conserved


Mass: 16839.662 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: A0A640KPN1
#8: Protein Rieske iron-sulfur protein, putative


Mass: 31494.869 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: A0A640KYQ2
#9: Protein LtaP35.0250, Hypothetical protein, conserved


Mass: 12990.755 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: A0A640KRZ1
#10: Protein Ubiquinol-cytochrome-c reductase-like protein


Mass: 7981.286 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: A0A640KNT3
#11: Protein LtaP27.0110, Hypothetical protein, conserved


Mass: 7997.269 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: A0A640KKU7

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Protein/peptide / Non-polymers , 2 types, 6 molecules Ll

#12: Protein/peptide unassigned helix


Mass: 2060.531 Da / Num. of mol.: 2
Fragment: unassigned helix with ATOM11 as the leading candidate
Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
#13: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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 III / 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: #1-#12 / Source: NATURAL
Molecular weightExperimental value: NO
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
1cryoSPARC4.7.0particle selection
7Coot0.9.6model fitting
8ISOLDE1.12model fitting
10PHENIX1.21.2_5419model refinement
14cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13544 / Symmetry type: POINT
RefinementHighest resolution: 3.02 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_d0.00242698
ELECTRON MICROSCOPYf_angle_d0.49758044
ELECTRON MICROSCOPYf_dihedral_angle_d10.92715298
ELECTRON MICROSCOPYf_chiral_restr0.0396110
ELECTRON MICROSCOPYf_plane_restr0.0067356

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