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- EMDB-21371: Single particle reconstruction of glucose isomerase from Streptom... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21371 | ||||||||||||||||||
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Title | Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||
![]() | Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||
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![]() | glucose isomerase / ISOMERASE | ||||||||||||||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
![]() | Bromberg R / Guo Y | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution cryo-EM reconstructions in the presence of substantial aberrations. Authors: Raquel Bromberg / Yirui Guo / Dominika Borek / Zbyszek Otwinowski / ![]() Abstract: Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula ...Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments. #1: ![]() Title: High-resolution cryo-EM reconstructions in the presence of substantial aberrations Authors: Bromberg R / Guo Y / Borek D / Otwinowski Z | ||||||||||||||||||
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 | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
Images | ![]() | 148.9 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 360.4 KB | Display | ![]() |
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Full document | ![]() | 359.9 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vrsMC ![]() 6vsaC ![]() 6vscC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.0 TB Data #1: Unaligned multiframe data for xylose isomerase (glucose isomerase) [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
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Annotation | Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : glucose isomerase
Entire | Name: glucose isomerase |
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Components |
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-Supramolecule #1: glucose isomerase
Supramolecule | Name: glucose isomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 172.9 KDa |
-Macromolecule #1: xylose isomerase
Macromolecule | Name: xylose isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: xylose isomerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 43.283297 KDa |
Sequence | String: MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP FGSSDSEREE HVKRFRQALD DTGMKVPMA TTNLFTHPVF KDGGFTANDR DVRRYALRKT IRNIDLAVEL GAETYVAWGG REGAESGGAK DVRDALDRMK E AFDLLGEY ...String: MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP FGSSDSEREE HVKRFRQALD DTGMKVPMA TTNLFTHPVF KDGGFTANDR DVRRYALRKT IRNIDLAVEL GAETYVAWGG REGAESGGAK DVRDALDRMK E AFDLLGEY VTSQGYDIRF AIEPKPNEPR GDILLPTVGH ALAFIERLER PELYGVNPEV GHEQMAGLNF PHGIAQALWA GK LFHIDLN GQNGIKYDQD LRFGAGDLRA AFWLVDLLES AGYSGPRHFD FKPPRTEDFD GVWASAAGCM RNYLILKERA AAF RADPEV QEALRASRLD ELARPTAADG LQALLDDRSA FEEFDVDAAA ARGMAFERLD QLAMDHLLGA RG UniProtKB: Xylose isomerase |
-Macromolecule #2: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 16 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 40 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 20.0 mM / Component - Name: HEPES |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS TALOS |
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Alignment procedure | Basic - Residual tilt: 5.3 mrad |
Details | The goal of the experiment was to show that it is possible to perform high resolution reconstruction in the presence of higher order aberrations. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-200 / Number grids imaged: 1 / Number real images: 202 / Average exposure time: 100.0 sec. / Average electron dose: 120.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | COOT was crucial as well. |
Refinement | Space: RECIPROCAL / Protocol: OTHER / Target criteria: REFMAC |
Output model | ![]() PDB-6vrs: |