+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5623 | |||||||||
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Title | 3D reconstruction of archaeal 20S proteasome | |||||||||
Map data | 3D reconstruction of archaeal 20S proteasome | |||||||||
Sample |
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Keywords | Thermoplasma acidophilum 20S proteasome | |||||||||
Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Li X / Mooney P / Zheng S / Booth C / Braunfeld MB / Gubbens S / Agard DA / Cheng Y | |||||||||
Citation | Journal: Nat Methods / Year: 2013 Title: Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Authors: Xueming Li / Paul Mooney / Shawn Zheng / Christopher R Booth / Michael B Braunfeld / Sander Gubbens / David A Agard / Yifan Cheng / Abstract: In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of ...In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5623.map.gz | 56.9 MB | EMDB map data format | |
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Header (meta data) | emd-5623-v30.xml emd-5623.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_5623_1.jpg | 301.5 KB | ||
Others | emd_5623_additional_1.map.gz emd_5623_half_map_1.map.gz emd_5623_half_map_2.map.gz | 14.2 MB 14.3 MB 14.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5623 | HTTPS FTP |
-Validation report
Summary document | emd_5623_validation.pdf.gz | 366.9 KB | Display | EMDB validaton report |
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Full document | emd_5623_full_validation.pdf.gz | 366.5 KB | Display | |
Data in XML | emd_5623_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5623 | HTTPS FTP |
-Related structure data
Related structure data | 3j9iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5623.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of archaeal 20S proteasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 5623 additional 1.map
File | emd_5623_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 5623 half map 1.map
File | emd_5623_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 5623 half map 2.map
File | emd_5623_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Thermoplasma acidophilum 20S proteasome
Entire | Name: Thermoplasma acidophilum 20S proteasome |
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Components |
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-Supramolecule #1000: Thermoplasma acidophilum 20S proteasome
Supramolecule | Name: Thermoplasma acidophilum 20S proteasome / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 28mer / Number unique components: 1 |
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Molecular weight | Experimental: 700 KDa |
-Macromolecule #1: 20S proteasome
Macromolecule | Name: 20S proteasome / type: protein_or_peptide / ID: 1 / Oligomeric state: 28mer / Recombinant expression: Yes |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Experimental: 700 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pREAR-A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: Quantifoil grid |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | Images were recorded in dose-fractionated format using K2 Summit operated in counting and super-resolution mode. Motion correction was performed for each image. |
Date | Jun 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 600 / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | GPU enhanced FREALIGN |
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CTF correction | Details: each particle |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 126729 |