+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34743 | ||||||||||||||||||||||||
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Title | GroEL on Quantifoil grid | ||||||||||||||||||||||||
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Sample |
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Biological species | Escherichia coli (E. coli) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | ||||||||||||||||||||||||
Authors | Fujita J / Makino F / Asahara H / Moriguchi M / Kumano S / Anzai I / Kishikawa J / Matsuura Y / Kato T / Namba K / Inoue T | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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Citation | Journal: Sci Rep / Year: 2023 Title: Epoxidized graphene grid for highly efficient high-resolution cryoEM structural analysis. Authors: Junso Fujita / Fumiaki Makino / Haruyasu Asahara / Maiko Moriguchi / Shota Kumano / Itsuki Anzai / Jun-Ichi Kishikawa / Yoshiharu Matsuura / Takayuki Kato / Keiichi Namba / Tsuyoshi Inoue / Abstract: Functionalization of graphene is one of the most important fundamental technologies in a wide variety of fields including industry and biochemistry. We have successfully achieved a novel oxidative ...Functionalization of graphene is one of the most important fundamental technologies in a wide variety of fields including industry and biochemistry. We have successfully achieved a novel oxidative modification of graphene using photoactivated ClO as a mild oxidant and confirmed the oxidized graphene grid is storable with its functionality for at least three months under N atmosphere. Subsequent chemical functionalization enabled us to develop an epoxidized graphene grid (EG-grid™), which effectively adsorbs protein particles for electron cryomicroscopy (cryoEM) image analysis. The EG-grid dramatically improved the particle density and orientation distribution. The density maps of GroEL and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were reconstructed at 1.99 and 2.16 Å resolution from only 504 and 241 micrographs, respectively. A sample solution of 0.1 mg ml was sufficient to reconstruct a 3.10 Å resolution map of SARS-CoV-2 spike protein from 1163 micrographs. The map resolutions of β-galactosidase and apoferritin easily reached 1.81 Å and 1.29 Å resolution, respectively, indicating its atomic-resolution imaging capability. Thus, the EG-grid will be an extremely powerful tool for highly efficient high-resolution cryoEM structural analysis of biological macromolecules. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34743.map.gz | 20.9 MB | EMDB map data format | |
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Header (meta data) | emd-34743-v30.xml emd-34743.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34743_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_34743.png | 209.2 KB | ||
Masks | emd_34743_msk_1.map | 178 MB | Mask map | |
Others | emd_34743_additional_1.map.gz emd_34743_half_map_1.map.gz emd_34743_half_map_2.map.gz | 106.5 MB 141.1 MB 141.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34743 | HTTPS FTP |
-Validation report
Summary document | emd_34743_validation.pdf.gz | 826 KB | Display | EMDB validaton report |
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Full document | emd_34743_full_validation.pdf.gz | 825.6 KB | Display | |
Data in XML | emd_34743_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_34743_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34743 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34743 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34743.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.867 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34743_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Filtered map
File | emd_34743_additional_1.map | ||||||||||||
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Annotation | Filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34743_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34743_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL
Entire | Name: GroEL |
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Components |
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-Supramolecule #1: GroEL
Supramolecule | Name: GroEL / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all Details: The sample was purchased from TaKaRa Bio Inc. (Product code 7330). |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 802 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG ...String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG KEGVITVEDG TGLQDELDVV EGMQFDRGYL SPYFINKPET GAVELESPFI LLADKKISNI REMLPVLEAV AKAGKPLLII AEDVEGEALA TLVVNTMRGI VKVAAVKAPG FGDRRKAMLQ DIATLTGGTV ISEEIGMELE KATLEDLGQA KRVVINKDTT TIIDGVGEEA AIQGRVAQIR QQIEEATSDY DREKLQERVA KLAGGVAVIK VGAATEVEMK EKKARVEDAL HATRAAVEEG VVAGGGVALI RVASKLADLR GQNEDQNVGI KVALRAMEAP LRQIVLNCGE EPSVVANTVK GGDGNYGYNA ATEEYGNMID MGILDPTKVT RSALQYAASV AGLMITTECM VTDLPKNDAA DLGAAGGMGG MGGMGGMM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.3 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |