+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27579 | |||||||||
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Title | Human Brain Glyceraldehyde 3-phosphate dehydrogenase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human brain / GAPDH / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) 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 / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / disordered domain specific binding / NAD binding / microtubule cytoskeleton / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / neuron apoptotic process / vesicle / killing of cells of another organism / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Tringides ML | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Life Sci Alliance / Year: 2023 Title: A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes. Authors: Marios L Tringides / Zhemin Zhang / Christopher E Morgan / Chih-Chia Su / Edward W Yu / Abstract: We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual ...We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27579.map.gz | 4.1 MB | EMDB map data format | |
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Header (meta data) | emd-27579-v30.xml emd-27579.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_27579.png | 460.4 KB | ||
Filedesc metadata | emd-27579.cif.gz | 4.8 KB | ||
Others | emd_27579_half_map_1.map.gz emd_27579_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27579 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27579 | HTTPS FTP |
-Validation report
Summary document | emd_27579_validation.pdf.gz | 848.3 KB | Display | EMDB validaton report |
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Full document | emd_27579_full_validation.pdf.gz | 847.9 KB | Display | |
Data in XML | emd_27579_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_27579_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27579 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27579 | HTTPS FTP |
-Related structure data
Related structure data | 8dnsMC 8dnmC 8dnoC 8dnpC 8dnuC M: atomic model generated by this map 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_27579.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27579_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27579_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 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 / Number of copies: 4 / Enantiomer: LEVO EC number: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 36.099168 KDa |
Sequence | String: MGKVKVGVNG FGRIGRLVTR AAFNSGKVDI VAINDPFIDL NYMVYMFQYD STHGKFHGTV KAENGKLVIN GNPITIFQER DPSKIKWGD AGAEYVVEST GVFTTMEKAG AHLQGGAKRV IISAPSADAP MFVMGVNHEK YDNSLKIISN ASCTTNCLAP L AKVIHDNF ...String: MGKVKVGVNG FGRIGRLVTR AAFNSGKVDI VAINDPFIDL NYMVYMFQYD STHGKFHGTV KAENGKLVIN GNPITIFQER DPSKIKWGD AGAEYVVEST GVFTTMEKAG AHLQGGAKRV IISAPSADAP MFVMGVNHEK YDNSLKIISN ASCTTNCLAP L AKVIHDNF GIVEGLMTTV HAITATQKTV DGPSGKLWRD GRGALQNIIP ASTGAAKAVG KVIPELNGKL TGMAFRVPTA NV SVVDLTC RLEKPAKYDD IKKVVKQASE GPLKGILGYT EHQVVSSDFN SDTHSSTFDA GAGIALNDHF VKLISWYDNE FGY SNRVVD LMAHMASKE UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.706 µm / Nominal defocus min: 1.212 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8982 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |