+Open data
-Basic information
Entry | Database: PDB / ID: 7jrg | ||||||
---|---|---|---|---|---|---|---|
Title | Plant Mitochondrial complex III2 from Vigna radiata | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / mitochondria / respiration / bioenergetics / plants | ||||||
Function / homology | Function and homology information protein processing involved in protein targeting to mitochondrion / : / 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 / : / 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 | ||||||
Biological species | Vigna radiata var. radiata (mung bean) Vigna radiata (mung bean) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Maldonado, M. / Letts, J.A. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jrg.cif.gz | 742.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jrg.ent.gz | 625.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jrg_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jrg_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7jrg_validation.xml.gz | 137.4 KB | Display | |
Data in CIF | 7jrg_validation.cif.gz | 196.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jrg ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jrg | HTTPS FTP |
-Related structure data
Related structure data | 22445MC 7jroC 7jrpC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10586 (Title: Cryo electron micrographs of digitonin-solubilized, amphipol-stabilized, sucrose-gradient-purified V. radiata mitochondrial membranes - mixed fraction containing CI*, CIII2 and SC III2+IV Data size: 6.7 TB Data #1: Raw movies of mixed sample used for determination of mung bean respiratory CI*, CIII2, CIV and SC III2+IV [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 5 types, 10 molecules AMBNCODPKW
#1: Protein | 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 | 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 | Mass: 44353.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) #4: Protein | 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 | Mass: 8948.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) |
---|
-Cytochrome b-c1 complex subunit ... , 5 types, 10 molecules EQFRGSHTJV
#5: Protein | 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 | 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 | 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 | 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 | 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 |
---|
-Non-polymers , 6 types, 37 molecules
#11: Chemical | #12: Chemical | #13: Chemical | ChemComp-CDL / #14: Chemical | ChemComp-HEM / #15: Chemical | ChemComp-3PE / #16: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial Respiratory Complex III2 / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.485 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Vigna radiata (mung bean) / Organelle: mitochondria / Tissue: hypocotyl | |||||||||||||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 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 support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 60010 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 150000000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48111 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 67 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building |
|