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- EMDB-9225: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9225 | |||||||||
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Title | Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome | |||||||||
![]() | State EB map of substrate-engaged human proteasome low pass-filtered to 3 Angstrom, without amplitude correction | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Mao YD | |||||||||
![]() | ![]() Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao / ![]() ![]() Abstract: The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of ...The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 745.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.1 KB 15.1 KB | Display Display | ![]() |
Images | ![]() | 39.2 KB | ||
Others | ![]() ![]() | 752.5 MB 730.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9215C ![]() 9216C ![]() 9217C ![]() 9218C ![]() 9219C ![]() 9220C ![]() 9221C ![]() 9222C ![]() 9223C ![]() 9224C ![]() 9226C ![]() 9227C ![]() 9228C ![]() 9229C ![]() 6msbC ![]() 6msdC ![]() 6mseC ![]() 6msgC ![]() 6mshC ![]() 6msjC ![]() 6mskC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 13.9 TB Data #1: Drift-corrected frame-averaged super-counting mode micrographs and extracted particles of substrate-engaged human 26S proteasome [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | State EB map of substrate-engaged human proteasome low pass-filtered to 3 Angstrom, without amplitude correction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.685 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: State EB map of substrate-engaged human proteasome low...
File | emd_9225_additional_1.map | ||||||||||||
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Annotation | State EB map of substrate-engaged human proteasome low pass-filtered to 3 Angstrom, with amplitude corrected by a B-factor of -35 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered, uncorrected raw EB map
File | emd_9225_additional_2.map | ||||||||||||
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Annotation | Unfiltered, uncorrected raw EB map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Proteasome
Entire | Name: Proteasome |
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Components |
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-Supramolecule #1: Proteasome
Supramolecule | Name: Proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242965 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: PROJECTION MATCHING |