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Yorodumi- EMDB-33528: Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas rein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33528 | |||||||||||||||
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Title | Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas reinhardtii | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information protein import into chloroplast stroma / chloroplast inner membrane / chloroplast outer membrane / chloroplast membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / membrane => GO:0016020 / hydrolase activity / GTP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||||||||
Authors | Liu H / Li AJ / Liu ZF | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Nature / Year: 2023 Title: Architecture of chloroplast TOC-TIC translocon supercomplex. Authors: Hao Liu / Anjie Li / Jean-David Rochaix / Zhenfeng Liu / Abstract: Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (the TOC and TIC complexes, respectively) to import thousands of different nuclear-encoded proteins from the ...Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (the TOC and TIC complexes, respectively) to import thousands of different nuclear-encoded proteins from the cytosol. Although previous studies indicated that the TOC and TIC complexes may assemble into larger supercomplexes, the overall architectures of the TOC-TIC supercomplexes and the mechanism of preprotein translocation are unclear. Here we report the cryo-electron microscopy structure of the TOC-TIC supercomplex from Chlamydomonas reinhardtii. The major subunits of the TOC complex (Toc75, Toc90 and Toc34) and TIC complex (Tic214, Tic20, Tic100 and Tic56), three chloroplast translocon-associated proteins (Ctap3, Ctap4 and Ctap5) and three newly identified small inner-membrane proteins (Simp1-3) have been located in the supercomplex. As the largest protein, Tic214 traverses the inner membrane, the intermembrane space and the outer membrane, connecting the TOC complex with the TIC proteins. An inositol hexaphosphate molecule is located at the Tic214-Toc90 interface and stabilizes their assembly. Four lipid molecules are located within or above an inner-membrane funnel formed by Tic214, Tic20, Simp1 and Ctap5. Multiple potential pathways found in the TOC-TIC supercomplex may support translocation of different substrate preproteins into chloroplasts. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33528.map.gz | 497.4 MB | EMDB map data format | |
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Header (meta data) | emd-33528-v30.xml emd-33528.xml | 34.2 KB 34.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33528_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_33528.png | 72.7 KB | ||
Others | emd_33528_half_map_1.map.gz emd_33528_half_map_2.map.gz | 927.1 MB 927.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33528 | HTTPS FTP |
-Related structure data
Related structure data | 7xziMC 7xzjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33528.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33528_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33528_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : a membrane protein complex
+Supramolecule #1: a membrane protein complex
+Macromolecule #1: Ctap3
+Macromolecule #2: Ctap4
+Macromolecule #3: Ctap5
+Macromolecule #4: Toc75
+Macromolecule #5: Toc90
+Macromolecule #6: Tic214
+Macromolecule #7: Protein TIC 20
+Macromolecule #8: Tic15
+Macromolecule #9: Simp3
+Macromolecule #10: Tic100
+Macromolecule #11: Tic56
+Macromolecule #12: Toc34
+Macromolecule #13: Simp2
+Macromolecule #14: Unknown peptide
+Macromolecule #15: Digitonin
+Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #17: HEXADECANE
+Macromolecule #18: DODECANE
+Macromolecule #19: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7xzi: |