+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31890 | |||||||||
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Title | Cryo-EM structure of Chlamydomonas TOC-TIC supercomplex | |||||||||
Map data | Composite map | |||||||||
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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Wu J / Yan Z / Jin Z / Zhang Y | |||||||||
Funding support | 1 items
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Citation | Journal: Cell / Year: 2022 Title: Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes. Authors: Zeyu Jin / Li Wan / Yuqi Zhang / Xuecheng Li / Yong Cao / Haobin Liu / Shengyao Fan / Du Cao / Zhengmao Wang / Xiaobo Li / Junmin Pan / Meng-Qiu Dong / Jianping Wu / Zhen Yan / Abstract: The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular ...The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular identities and assembly remain unclear. Here, we report a cryoelectron microscopy structure of TOC-TIC supercomplex from Chlamydomonas, containing a total of 14 identified components. The preprotein-conducting pore of TOC is a hybrid β-barrel co-assembled by Toc120 and Toc75, while the potential translocation path of TIC is formed by transmembrane helices from Tic20 and YlmG, rather than a classic model of Tic110. A rigid intermembrane space (IMS) scaffold bridges two chloroplast membranes, and a large hydrophilic cleft on the IMS scaffold connects TOC and TIC, forming a pathway for preprotein translocation. Our study provides structural insights into the TOC-TIC supercomplex composition, assembly, and preprotein translocation mechanism, and lays a foundation to interpret the evolutionary conservation and diversity of this fundamental translocon machinery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31890.map.gz | 195.8 MB | EMDB map data format | |
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Header (meta data) | emd-31890-v30.xml emd-31890.xml | 49.6 KB 49.6 KB | Display Display | EMDB header |
Images | emd_31890.png | 119.6 KB | ||
Others | emd_31890_additional_1.map.gz emd_31890_additional_2.map.gz emd_31890_additional_3.map.gz emd_31890_additional_4.map.gz emd_31890_additional_5.map.gz emd_31890_additional_6.map.gz emd_31890_half_map_1.map.gz emd_31890_half_map_2.map.gz | 204 MB 202.5 MB 201.4 MB 202 MB 193 MB 184.2 MB 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31890 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31890 | HTTPS FTP |
-Related structure data
Related structure data | 7vcfMC 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_31890.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Map1 (Overall map)
File | emd_31890_additional_1.map | ||||||||||||
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Annotation | Map1 (Overall map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map4 (TIC IMS region map)
File | emd_31890_additional_2.map | ||||||||||||
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Annotation | Map4 (TIC IMS region map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map2 (TOCL region map)
File | emd_31890_additional_3.map | ||||||||||||
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Annotation | Map2 (TOCL region map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map3 (TOCS region map)
File | emd_31890_additional_4.map | ||||||||||||
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Annotation | Map3 (TOCS region map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite map (deepEMhancer)
File | emd_31890_additional_5.map | ||||||||||||
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Annotation | Composite map (deepEMhancer) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map5 (TIC YlmG map)
File | emd_31890_additional_6.map | ||||||||||||
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Annotation | Map5 (TIC YlmG map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall map half1
File | emd_31890_half_map_1.map | ||||||||||||
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Annotation | Overall map half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall map half2
File | emd_31890_half_map_2.map | ||||||||||||
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Annotation | Overall map half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TOC-TIC supercomplex
+Supramolecule #1: TOC-TIC supercomplex
+Macromolecule #1: Tic214
+Macromolecule #2: Toc75
+Macromolecule #3: Toc52
+Macromolecule #4: Tic13
+Macromolecule #5: Toc120
+Macromolecule #6: Toc34
+Macromolecule #7: YlmG
+Macromolecule #8: Toc39
+Macromolecule #9: Toc10
+Macromolecule #10: Tic12
+Macromolecule #11: Unknown fragment
+Macromolecule #12: Tic35
+Macromolecule #13: Tic56
+Macromolecule #14: Tic100
+Macromolecule #15: Tic20-Venus-Flag
+Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #17: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 82000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.0) / Number images used: 595638 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |