+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27580 | |||||||||
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Title | Human Brain Glutamine Synthetase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human brain / Glutamine Synthetase / ligase | |||||||||
Function / homology | Function and homology information protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity ...protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / glutamate catabolic process / glial cell projection / response to glucose / cellular response to starvation / ribosome biogenesis / cell body / angiogenesis / cell population proliferation / endoplasmic reticulum / mitochondrion / extracellular exosome / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 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_27580.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-27580-v30.xml emd-27580.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_27580.png | 645.1 KB | ||
Filedesc metadata | emd-27580.cif.gz | 5 KB | ||
Others | emd_27580_half_map_1.map.gz emd_27580_half_map_2.map.gz | 151.5 MB 151.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27580 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27580 | HTTPS FTP |
-Validation report
Summary document | emd_27580_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27580_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27580_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_27580_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27580 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27580 | HTTPS FTP |
-Related structure data
Related structure data | 8dnuMC 8dnmC 8dnoC 8dnpC 8dnsC 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_27580.map.gz / Format: CCP4 / Size: 9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_27580_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27580_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Glutamine Synthetase
Entire | Name: Glutamine Synthetase |
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Components |
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-Supramolecule #1: Glutamine Synthetase
Supramolecule | Name: Glutamine Synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.118402 KDa |
Sequence | String: MTTSASSHLN KGIKQVYMSL PQGEKVQAMY IWIDGTGEGL RCKTRTLDSE PKCVEELPEW NFDGSSTLQS EGSNSDMYLV PAAMFRDPF RKDPNKLVLC EVFKYNRRPA ETNLRHTCKR IMDMVSNQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String: MTTSASSHLN KGIKQVYMSL PQGEKVQAMY IWIDGTGEGL RCKTRTLDSE PKCVEELPEW NFDGSSTLQS EGSNSDMYLV PAAMFRDPF RKDPNKLVLC EVFKYNRRPA ETNLRHTCKR IMDMVSNQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD RAYGRDIVEA HYRACLYAGV KIAGTNAEVM PAQWEFQIGP CEGISMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL KYIEEAIEKL SKRHQYHIRA YDPKGGLDNA RRLTGFHETS NINDFSAGVA NRS ASIRIP RTVGQEKKGY FEDRRPSANC DPFSVTEALI RTCLLNETGD EPFQYKN UniProtKB: Glutamine synthetase |
-Macromolecule #2: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-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: 35.3 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: 1.6580000000000001 µm / Nominal defocus min: 0.216 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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27886 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |