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- EMDB-8741: Thermoplasma acidophilum 20S Proteasome using 200keV with stage p... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8741 | |||||||||
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Title | Thermoplasma acidophilum 20S Proteasome using 200keV with stage position | |||||||||
![]() | Final sharpened map of T. acidophilum 20S proteasome collected using stage position navigation | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Herzik Jr MA / Wu M / Lander GC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. Authors: Mark A Herzik / Mengyu Wu / Gabriel C Lander / ![]() Abstract: Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible ...Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules. | |||||||||
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 | ![]() | 59.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.5 KB 22.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 38.9 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() ![]() | 59 MB 409.8 MB 409.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vy3MC ![]() 8742C ![]() 8743C ![]() 5vy4C ![]() 5vy5C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 1.1 TB Data #1: Raw, unaligned movie stacks of T. acidophilum 20S proteasome core acquired on a Talos Arctica using a K2 direct electron detector - stage position used for exposure navigation [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final sharpened map of T. acidophilum 20S proteasome collected using stage position navigation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map of T. acidophilum 20S proteasome collected...
File | emd_8741_additional.map | ||||||||||||
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Annotation | Unsharpened map of T. acidophilum 20S proteasome collected using stage position navigation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Thermoplasma acidophilum 20S Proteasome, odd half map
File | emd_8741_half_map_1.map | ||||||||||||
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Annotation | Thermoplasma acidophilum 20S Proteasome, odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Thermoplasma acidophilum 20S Proteasome, even half map
File | emd_8741_half_map_2.map | ||||||||||||
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Annotation | Thermoplasma acidophilum 20S Proteasome, even half map | ||||||||||||
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 #1: Thermoplasma acidophilum 20S proteasome
Supramolecule | Name: Thermoplasma acidophilum 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Thermoplasma acidophilum 20S proteasome purified from Escherichia coli |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 24.776281 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: RAITVFSPDG RLFQVEYARE AVKKGSTALG MKFANGVLLI SDKKVRSRLI EQNSIEKIQL IDDYVAAVTS GLVADARVLV DFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG K DAVVSFLE ...String: RAITVFSPDG RLFQVEYARE AVKKGSTALG MKFANGVLLI SDKKVRSRLI EQNSIEKIQL IDDYVAAVTS GLVADARVLV DFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG K DAVVSFLE REYKENLPEK EAVTLGIKAL KSSLEEGEEL KAPEIASITV GNKYRIYDQE EVKKFL UniProtKB: ![]() |
-Macromolecule #2: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 22.294848 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: TTTVGITLKD AVIMATERRV TMENFIMHKN GKKLFQIDTY TGMTIAGLVG DAQVLVRYMK AELELYRLQR RVNMPIEAVA TLLSNMLNQ VKYMPYMVQL LVGGIDTAPH VFSIDAAGGS VEDIYASTGS GSPFVYGVLE SQYSEKMTVD EGVDLVIRAI S AAKQRDSA ...String: TTTVGITLKD AVIMATERRV TMENFIMHKN GKKLFQIDTY TGMTIAGLVG DAQVLVRYMK AELELYRLQR RVNMPIEAVA TLLSNMLNQ VKYMPYMVQL LVGGIDTAPH VFSIDAAGGS VEDIYASTGS GSPFVYGVLE SQYSEKMTVD EGVDLVIRAI S AAKQRDSA SGGMIDVAVI TRKDGYVQLP TDQIESRIRK LGLIL UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.009000000000000001 kPa / Details: 15 Watts | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: 3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-68 / Number grids imaged: 1 / Number real images: 629 / Average exposure time: 17.0 sec. / Average electron dose: 65.0 e/Å2 Details: Images were collected using stage position navigation to target exposure. |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 153429 Details: Template-based particle picking was performed using templates generated from reference-free 2D classification of an initial set of automated particle picks. |
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Startup model | Type of model: EMDB MAP EMDB ID: ![]() 6283 Details: Initial model was low-passed filtered to 60 Angstrom resolution |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral![]() |
Details | Movies were collected in super-resolution mode and Fourier-binned by two prior to motion correction and dose weighting using MotionCor2 program. |
FSC plot (resolution estimation)![]() | ![]() |
-Atomic model buiding 1
Details | Starting model was generated by stripping PDB entry 1YAR of all ligands and alternate conformations, then refining into the EM density using imposed symmetry while adjusting weighting/scoring according to estimated map resolution. The top 10 generated models (ranked based on quality metrics) were real-space refined using Phenix software. |
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Refinement | Space: REAL / Protocol: OTHER / Overall B value: 101 / Target criteria: Maximum Likelihood |
Output model | ![]() PDB-5vy3: |