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- EMDB-45137: Structure of endogenous Actin filament from rat model of Alzheime... -

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Basic information

Entry
Database: EMDB / ID: EMD-45137
TitleStructure of endogenous Actin filament from rat model of Alzheimer's disease
Map dataMain sharpened map
Sample
  • Tissue: glutamine synthetase
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION
KeywordsGlutamine synthetase / LIGASE
Function / homology
Function and homology information


Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / intracellular ammonium homeostasis / protein S-acyltransferase / protein palmitoylation / ammonia assimilation cycle / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration ...Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / intracellular ammonium homeostasis / protein S-acyltransferase / protein palmitoylation / ammonia assimilation cycle / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / dynein light chain binding / glutamate metabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / nickel cation binding / glial cell projection / response to glucose / axon terminus / positive regulation of synaptic transmission, glutamatergic / positive regulation of erythrocyte differentiation / positive regulation of epithelial cell proliferation / cellular response to starvation / cell projection / positive regulation of insulin secretion / ribosome biogenesis / myelin sheath / manganese ion binding / cell body / angiogenesis / perikaryon / cell population proliferation / magnesium ion binding / endoplasmic reticulum / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain ...: / 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 (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsKhalili Samani E / Keszei AFA / Mazhab-Jafari MT
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)419240 Canada
CitationJournal: Structure / Year: 2025
Title: Unveiling the structural proteome of an Alzheimer's disease rat brain model.
Authors: Elnaz Khalili Samani / S M Naimul Hasan / Matthew Waas / Alexander F A Keszei / Xiaoxiao Xu / Mahtab Heydari / Mary Elizabeth Hill / JoAnne McLaurin / Thomas Kislinger / Mohammad T Mazhab-Jafari /
Abstract: Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically ...Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically affected tissues often relies on mass spectrometry and proteomic analysis. Here, we utilized cryoelectron microscopy (cryo-EM) and the Build and Retrieve (BaR) method to investigate protein complexes' structural characteristics such as post-translational modification, active site occupancy, and arrested conformational state in Alzheimer's disease (AD) using brain lysate from a rat model (TgF344-AD). Our findings reveal novel insights into the architecture of these complexes, corroborated through mass spectrometry analysis. Interestingly, it has been shown that the dysfunction of these protein complexes extends beyond AD, implicating them in cancer, as well as other neurodegenerative disorders such as Parkinson's disease, Huntington's disease, and schizophrenia. By elucidating these structural details, our work not only enhances our understanding of disease pathology but also suggests new avenues for future approaches in therapeutic intervention.
History
DepositionMay 30, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45137.png

Downloads & links

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Map

FileDownload / File: emd_45137.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 250 pix.
= 257.5 Å		1.03 Å/pix.
x 250 pix.
= 257.5 Å		1.03 Å/pix.
x 250 pix.
= 257.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5479788 - 0.7430121
Average (Standard dev.)0.001382757 (±0.029203627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 257.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_45137_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45137_half_map_2.map
AnnotationHalf map B
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
  • Tissue: glutamine synthetase
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: glutamine synthetase

SupramoleculeName: glutamine synthetase / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: TgF344 / Organ: Brain

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 42.323777 KDa
SequenceString: MATSASSHLN KGIKQMYMNL PQGEKIQLMY IWVDGTGEGL RCKTRTLDCD PKCVEELPEW NFDGSSTFQS EGSNSDMYLH PVAMFRDPF RRDPNKLVFC EVFKYNRKPA ETNLRHSCKR IMDMVSSQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String:
MATSASSHLN KGIKQMYMNL PQGEKIQLMY IWVDGTGEGL RCKTRTLDCD PKCVEELPEW NFDGSSTFQS EGSNSDMYLH PVAMFRDPF RRDPNKLVFC EVFKYNRKPA ETNLRHSCKR IMDMVSSQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD KAYGRDIVEA HYRACLYAGI KITGTNAEVM PAQWEFQIGP CEGIRMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL RCIEEAIDKL SKRHQYHIRA YDPKGGLDNA RRLTGFHETS NINDFSAGVA NRS ASIRIP RIVGQEKKGY FEDRRPSANC DPYAVTEAIV RTCLLNETGD EPFQYKN

UniProtKB: Glutamine synthetase

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 20 / 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 stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Homemade / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsCytosolic fraction of rat brain

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12098
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

7u5n


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9c28:
Structure of endogenous Glutamine synthetase from rat model of Alzheimer's disease

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