+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32162 | ||||||||||||||||||||||||
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Title | GAPDH on EG-grid | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | GAPDH / Glyceraldehyde-3-phosphate dehydrogenase / HYDROLASE | ||||||||||||||||||||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex ...Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / microtubule cytoskeleton organization / cellular response to type II interferon / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / neuron apoptotic process / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / vesicle / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / membrane / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.16 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_32162.map.gz | 7.7 MB | EMDB map data format | |
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Header (meta data) | emd-32162-v30.xml emd-32162.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32162_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_32162.png | 73.4 KB | ||
Masks | emd_32162_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-32162.cif.gz | 5.5 KB | ||
Others | emd_32162_additional_1.map.gz emd_32162_half_map_1.map.gz emd_32162_half_map_2.map.gz | 66.3 MB 79.3 MB 79.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32162 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32162 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32162.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.813 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_32162_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered map
File | emd_32162_additional_1.map | ||||||||||||
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Annotation | Locally filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32162_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32162_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Glyceraldehyde-3-phosphate dehydrogenase
Entire | Name: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase |
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Components |
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-Supramolecule #1: Glyceraldehyde-3-phosphate dehydrogenase
Supramolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase
Macromolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GMGKVKVGVN GFGRIGRLVT RAAFNSGKVD IVAINDPFID LNYMVYMFQY DSTHGKFHGT VKAENGKLVI NGNPITIFQE RDPSKIKWGD AGAEYVVEST GVFTTMEKAG AHLQGGAKRV IISAPSADAP MFVMGVNHEK YDNSLKIISN ASCTTNCLAP LAKVIHDNFG ...String: GMGKVKVGVN GFGRIGRLVT RAAFNSGKVD IVAINDPFID LNYMVYMFQY DSTHGKFHGT VKAENGKLVI NGNPITIFQE RDPSKIKWGD AGAEYVVEST GVFTTMEKAG AHLQGGAKRV IISAPSADAP MFVMGVNHEK YDNSLKIISN ASCTTNCLAP LAKVIHDNFG IVEGLMTTVH AITATQKTVD GPSGKLWRDG RGALQNIIPA STGAAKAVGK VIPELNGKLT GMAFRVPTAN VSVVDLTCRL EKPAKYDDIK KVVKQASEGP LKGILGYTEH QVVSSDFNSD THSSTFDAGA GIALNDHFVK LISWYDNEFG YSNRVVDLMA HMASKE UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 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 chemically oxidized and modified. | ||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.8 sec. / Average electron dose: 40.0 e/Å2 |