+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25921 | |||||||||||||||||||||
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Title | CryoET of presequence protease single particle | |||||||||||||||||||||
Map data | Binned by 4 dose-compensated Tomo3D reconstruction from Appion-Protomo alignment | |||||||||||||||||||||
Sample |
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Keywords | presequence protease / mitochondrial proteostasis / PEPTIDE BINDING PROTEIN | |||||||||||||||||||||
Biological species | Escherichia phage EcSzw-2 (virus) | |||||||||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||||||||
Authors | Noble AJ / Liang W / Tang WJ | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Authors: Wenguang G Liang / Juwina Wijaya / Hui Wei / Alex J Noble / Jordan M Mancl / Swansea Mo / David Lee / John V Lin King / Man Pan / Chang Liu / Carla M Koehler / Minglei Zhao / Clinton S ...Authors: Wenguang G Liang / Juwina Wijaya / Hui Wei / Alex J Noble / Jordan M Mancl / Swansea Mo / David Lee / John V Lin King / Man Pan / Chang Liu / Carla M Koehler / Minglei Zhao / Clinton S Potter / Bridget Carragher / Sheng Li / Wei-Jen Tang / Abstract: Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other ...Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption. Thereby, we elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3-4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives a rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25921.map.gz | 2.2 GB | EMDB map data format | |
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Header (meta data) | emd-25921-v30.xml emd-25921.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_25921.png | 185.4 KB | ||
Filedesc metadata | emd-25921.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25921 | HTTPS FTP |
-Related structure data
Related structure data | 6xosC 6xotC 6xouC 6xovC C: citing same article (ref.) |
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EM raw data | EMPIAR-10929 (Title: CryoET of presequence protease single particle / Data size: 25.4 Data #1: Unaligned K2 tilt image frame stacks [micrographs - multiframe] Data #2: Binned by 4 tomograms from all 7 tilt-series [reconstructed volumes]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25921.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Binned by 4 dose-compensated Tomo3D reconstruction from Appion-Protomo alignment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.324 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human presequence protease
Entire | Name: Human presequence protease |
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Components |
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-Supramolecule #1: Human presequence protease
Supramolecule | Name: Human presequence protease / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia phage EcSzw-2 (virus) |
Molecular weight | Theoretical: 117 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.5 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 4.0 e/Å2 / Details: See EMPIAR entry for details. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Number images used: 36 |
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