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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6246 | |||||||||
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Title | Thermoplasma acidophilum 20S proteasome | |||||||||
![]() | Thermoplasma acidophilum 20S proteasome. Reconstruction determined from the first 3,000 particles of a dataset used to calculate map EMD-5623. | |||||||||
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![]() | T. acidophilum 20S proteasome | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Li X / Cheng Y | |||||||||
![]() | ![]() Title: Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Authors: Frank DiMaio / Yifan Song / Xueming Li / Matthias J Brunner / Chunfu Xu / Vincent Conticello / Edward Egelman / Thomas Marlovits / Yifan Cheng / David Baker / ![]() ![]() ![]() Abstract: We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local ...We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems. | |||||||||
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 | ![]() | 59 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.5 KB 8.5 KB | Display Display | ![]() |
Images | ![]() ![]() | 61.9 KB 5.1 KB | ||
Others | ![]() ![]() | 56.7 MB 56.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.8 KB | Display | ![]() |
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Full document | ![]() | 77.9 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Thermoplasma acidophilum 20S proteasome. Reconstruction determined from the first 3,000 particles of a dataset used to calculate map EMD-5623. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 6246 half map 1.map
File | emd_6246_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6246 half map 2.map
File | emd_6246_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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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: 28-mer / Number unique components: 1 |
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Molecular weight | Experimental: 700 KDa |
-Macromolecule #1: Thermoplasma acidophilum 20S proteasome
Macromolecule | Name: Thermoplasma acidophilum 20S proteasome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: 28-mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 700 KDa |
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
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | FREALIGN |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: OTHER / Number images used: 3000 |