[English] 日本語
Yorodumi- EMDB-32325: Cryo-EM structure of Tetrahymena thermophila mitochondrial comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32325 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial complex IV, composite dimer model | |||||||||
Map data | Tetrahymena thermophila electron transport chain complex IV dimer composite map. Combined by Phenix from 3.02 angstrom protomer map focus-refined in cryosparc. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase ...thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase / antiporter activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport / monoatomic ion channel activity / nucleic acid binding / membrane => GO:0016020 / mitochondrial inner membrane / DNA-binding transcription factor activity / copper ion binding / heme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Zhou L / Maldonado M / Padavannil A / Letts J | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Science / Year: 2022 Title: Structures of 's respiratory chain reveal the diversity of eukaryotic core metabolism. Authors: Long Zhou / María Maldonado / Abhilash Padavannil / Fei Guo / James A Letts / Abstract: Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and ...Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII (Tt-SC I+III) and a structure of Tt-CIV. Tt-SC I+III (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM8-TIM13-like domain. Our structural and functional study of the respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_32325.map.gz | 451 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-32325-v30.xml emd-32325.xml | 87.1 KB 87.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32325_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_32325.png | 151.4 KB | ||
Masks | emd_32325_msk_1.map | 512 MB | Mask map | |
Others | emd_32325_half_map_1.map.gz emd_32325_half_map_2.map.gz | 474.8 MB 474.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32325 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32325 | HTTPS FTP |
-Validation report
Summary document | emd_32325_validation.pdf.gz | 915.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_32325_full_validation.pdf.gz | 914.6 KB | Display | |
Data in XML | emd_32325_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | emd_32325_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32325 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32325 | HTTPS FTP |
-Related structure data
Related structure data | 7w5zMC 7tghC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10882 (Title: Cryo electron micrographs of Tetrahymena thermophila solubilized mitochondrial membrane complexes - Glacios data Data size: 9.9 TB Data #1: Unaligned multiframe micrographs of Tetrahymena respiratory chain complexes [micrographs - multiframe] Data #2: Aligned motion corrected micrographs of Tetrahymena respiratory chain complexes [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_32325.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Tetrahymena thermophila electron transport chain complex IV dimer composite map. Combined by Phenix from 3.02 angstrom protomer map focus-refined in cryosparc. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_32325_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A for Tetrahymena thermophila electron transport...
File | emd_32325_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A for Tetrahymena thermophila electron transport chain complex IV2 protomer map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A for Tetrahymena thermophila electron transport...
File | emd_32325_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A for Tetrahymena thermophila electron transport chain complex IV2 protomer map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Cytochrome c oxidase dimer
+Supramolecule #1: Cytochrome c oxidase dimer
+Macromolecule #1: Unknown peptide
+Macromolecule #2: Transmembrane protein, putative
+Macromolecule #3: Unknown peptide
+Macromolecule #4: Unknown peptide
+Macromolecule #5: Uncharacterized protein
+Macromolecule #6: Protein transporter Sec61 alpha subunit
+Macromolecule #7: Cytochrome c oxidase subunit 1
+Macromolecule #8: Cytochrome c oxidase subunit 2
+Macromolecule #9: Ymf68
+Macromolecule #10: Cytochrome C oxidase subunit Vb protein
+Macromolecule #11: Transmembrane protein, putative
+Macromolecule #12: Cytochrome c oxidase subunit 6B
+Macromolecule #13: Cytochrome c oxidase subunit 6B-like
+Macromolecule #14: Transmembrane protein, putative
+Macromolecule #15: Transmembrane protein, putative
+Macromolecule #16: Cytochrome c oxidase subunit 7C
+Macromolecule #17: CTF/NF-I domain-containing protein
+Macromolecule #18: Oxoglutarate/malate translocator protein, putative
+Macromolecule #19: 2-oxoglutarate/malate carrier protein
+Macromolecule #20: Carrier protein
+Macromolecule #21: Tim10/DDP family zinc finger protein
+Macromolecule #22: Cytochrome c oxidase small TIM subunit 2
+Macromolecule #23: Cytochrome c oxidase small TIM subunit 3
+Macromolecule #24: Cytochrome c oxidase small TIM subunit 4
+Macromolecule #25: Cytochrome c oxidase small TIM subunit 5
+Macromolecule #26: Cytochrome c oxidase small TIM subunit 6
+Macromolecule #27: Chromosome condensation regulator RCC1 repeat protein
+Macromolecule #28: Iron-binding zinc finger CDGSH type protein
+Macromolecule #29: Cytochrome c oxidase acyl carrier-like subunit
+Macromolecule #30: Ymf67
+Macromolecule #31: Ymf70
+Macromolecule #32: Ymf75
+Macromolecule #33: Transmembrane protein, putative
+Macromolecule #34: Protein phosphatase 2C, putative
+Macromolecule #35: Cyclic nucleotide-binding domain protein
+Macromolecule #36: SURF1-like protein
+Macromolecule #37: TraB family protein
+Macromolecule #38: Transmembrane protein, putative
+Macromolecule #39: Cytochrome c oxidase subunit TT7
+Macromolecule #40: SURF1-like protein
+Macromolecule #41: Cytochrome c oxidase subunit TT9
+Macromolecule #42: Cytochrome c oxidase subunit TT10
+Macromolecule #43: Cytochrome c oxidase subunit TT11
+Macromolecule #44: Cytochrome c oxidase subunit TT12
+Macromolecule #45: Transmembrane protein, putative
+Macromolecule #46: Transmembrane protein, putative
+Macromolecule #47: Cytochrome c oxidase subunit TT15
+Macromolecule #48: Cytochrome c oxidase subunit TT16
+Macromolecule #49: Transmembrane protein, putative
+Macromolecule #50: Cytochrome c oxidase subunit TT18
+Macromolecule #51: Cytochrome c oxidase subunit TT19
+Macromolecule #52: Transmembrane protein, putative
+Macromolecule #53: Transmembrane protein, putative
+Macromolecule #54: Cytochrome c oxidase subunit TT22
+Macromolecule #55: Transmembrane protein, putative
+Macromolecule #56: Transmembrane protein, putative
+Macromolecule #57: Cytochrome c oxidase subunit TT25
+Macromolecule #58: Cytochrome c oxidase subunit TT26
+Macromolecule #59: HEME-A
+Macromolecule #60: COPPER (II) ION
+Macromolecule #61: MAGNESIUM ION
+Macromolecule #62: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #63: CARDIOLIPIN
+Macromolecule #64: ZINC ION
+Macromolecule #65: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
Details: Solution were made fresh from concentrated stocks, filtered and de-gassed before equilibration onto Superose6 column | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: 30 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III Details: incubation time before blotting: 60s blot time: 9s blot force: 25 offset: -2 incubation after blotting: 0s. |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 17478 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 56818 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-7w5z: |