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- PDB-7jrg: Plant Mitochondrial complex III2 from Vigna radiata -

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Basic information

Entry
Database: PDB / ID: 7jrg
TitlePlant Mitochondrial complex III2 from Vigna radiata
Components
  • (Cytochrome b-c1 complex subunit ...) x 5
  • Alpha-MPP
  • COB
  • Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
  • QCR10
  • cytochrome c1-2, heme protein, mitochondrial
KeywordsELECTRON TRANSPORT / mitochondria / respiration / bioenergetics / plants
Function / homology
Function and homology information


protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / mitochondrion ...protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / mitochondrion / proteolysis / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like ...Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 9 / Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 9 / Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Mitochondrial-processing peptidase subunit alpha / Cytochrome b-c1 complex subunit 6 / Cytochrome c1-2, heme protein, mitochondrial
Similarity search - Component
Biological speciesVigna radiata var. radiata (mung bean)
Vigna radiata (mung bean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMaldonado, M. / Letts, J.A.
CitationJournal: Elife / Year: 2021
Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants.
Authors: Maria Maldonado / Fei Guo / James A Letts /
Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
B: Alpha-MPP
C: COB
D: cytochrome c1-2, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6
J: cytochrome b-c1 complex subunit 9
K: QCR10
M: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
N: Alpha-MPP
O: COB
P: cytochrome c1-2, heme protein, mitochondrial
Q: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
S: cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 6
V: cytochrome b-c1 complex subunit 9
W: QCR10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,54257
Polymers538,44520
Non-polymers32,09837
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules AMBNCODPKW

#1: Protein Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1


Mass: 58711.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TWG4
#2: Protein Alpha-MPP / Inactive zinc metalloprotease alpha / Mitochondrial-processing peptidase subunit alpha


Mass: 54537.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3VF71
#3: Protein COB


Mass: 44353.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#4: Protein cytochrome c1-2, heme protein, mitochondrial


Mass: 33556.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3W199
#10: Protein QCR10


Mass: 8948.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)

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Cytochrome b-c1 complex subunit ... , 5 types, 10 molecules EQFRGSHTJV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 30051.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean)
References: UniProt: A0A1S3TB49, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 14392.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3U9J1
#7: Protein cytochrome b-c1 complex subunit 8


Mass: 8349.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3U9S5
#8: Protein Cytochrome b-c1 complex subunit 6


Mass: 8117.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3VHC0
#9: Protein cytochrome b-c1 complex subunit 9


Mass: 8203.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TQD2

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Non-polymers , 6 types, 37 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#13: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#14: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#15: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#16: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Details

Has ligand of interestN

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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: Mitochondrial Respiratory Complex III2 / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 0.485 MDa / Experimental value: NO
Source (natural)Organism: Vigna radiata (mung bean) / Organelle: mitochondria / Tissue: hypocotyl
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMsodium chlorideNaCl1
31 mMEDTA1
40.2 %digitonin1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 60010 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 86.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9816
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 150000000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48111 / Symmetry type: POINT
Atomic model buildingB value: 67 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-ID
16Q9E

6q9e

1
26HU9

6hu9

1

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