+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34106 | ||||||||||||||||||||||||
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Title | GroEL on EG-grid stored for 3 months after graphene oxidation | ||||||||||||||||||||||||
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Sample |
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Biological species | Escherichia coli (E. coli) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.06 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_34106.map.gz | 19.8 MB | EMDB map data format | |
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Header (meta data) | emd-34106-v30.xml emd-34106.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34106_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_34106.png | 230.1 KB | ||
Masks | emd_34106_msk_1.map | 178 MB | Mask map | |
Others | emd_34106_additional_1.map.gz emd_34106_half_map_1.map.gz emd_34106_half_map_2.map.gz | 110 MB 140.6 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34106 | HTTPS FTP |
-Validation report
Summary document | emd_34106_validation.pdf.gz | 784.7 KB | Display | EMDB validaton report |
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Full document | emd_34106_full_validation.pdf.gz | 784.3 KB | Display | |
Data in XML | emd_34106_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_34106_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34106 | 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_34106.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: 0.868 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34106_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Filtered map
File | emd_34106_additional_1.map | ||||||||||||
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Annotation | Filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34106_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34106_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) |
Sequence | String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENM GAQMVKEVAS KANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG I DKAVTAAV EELKALSVPC SDSKAIAQVG TISANSDETV GKLIAEAMDK ...String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENM GAQMVKEVAS KANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG I DKAVTAAV EELKALSVPC SDSKAIAQVG TISANSDETV GKLIAEAMDK VGKEGVITVE DG TGLQDEL DVVEGMQFDR GYLSPYFINK PETGAVELES PFILLADKKI SNIREMLPVL EAV AKAGKP LLIIAEDVEG EALATLVVNT MRGIVKVAAV KAPGFGDRRK AMLQDIATLT GGTV ISEEI GMELEKATLE DLGQAKRVVI NKDTTTIIDG VGEEAAIQGR VAQIRQQIEE ATSDY DREK LQERVAKLAG GVAVIKVGAA TEVEMKEKKA RVEDALHATR AAVEEGVVAG GGVALI RVA SKLADLRGQN EDQNVGIKVA LRAMEAPLRQ IVLNCGEEPS VVANTVKGGD GNYGYNA AT EEYGNMIDMG ILDPTKVTRS ALQYAASVAG LMITTECMVT DLPKNDAADL GAAGGMGG M GGMGGMM |
-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: GOLD / Mesh: 200 / Support film - Material: GRAPHENE Details: The graphene grid was oxidized and stored under nitrogen gas at room temperature for three months. Then the grid was chemically modified. | |||||||||
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: 2.6 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 |