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- EMDB-27580: Human Brain Glutamine Synthetase -

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Basic information

Entry
Database: EMDB / ID: EMD-27580
TitleHuman Brain Glutamine Synthetase
Map data
Sample
  • Complex: Glutamine Synthetase
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION
Keywordshuman 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 / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process ...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 / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain ...Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsTringides ML
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: 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
DepositionJul 11, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27580.png

Downloads & links

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Map

FileDownload / File: emd_27580.map.gz / Format: CCP4 / Size: 9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5036213 - 2.2693386
Average (Standard dev.)-0.000000000005505 (±0.22394356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin104115105
Dimensions138121141
Spacing141138121
CellA: 150.87001 Å / B: 147.66 Å / C: 129.47 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27580_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27580_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glutamine Synthetase

EntireName: Glutamine Synthetase
Components
  • Complex: Glutamine Synthetase
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Glutamine Synthetase

SupramoleculeName: Glutamine Synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: human (human)
Molecular weightTheoretical: 42.118402 KDa
SequenceString: 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

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6580000000000001 µm / Nominal defocus min: 0.216 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ojw

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27886

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