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- EMDB-26356: Cryo-EM Structure of Glutamine Synthetase -

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Basic information

Entry
Database: EMDB / ID: EMD-26356
TitleCryo-EM Structure of Glutamine Synthetase
Map data
Sample
  • Complex: Decamer of Glutamine Synthetase
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION
Function / homology
Function and homology information


Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity ...Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / angiogenesis / endoplasmic reticulum / mitochondrion / ATP binding / metal ion binding / 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 speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsMorgan CE / Yu EW / Zhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2022
Title: Toward structural-omics of the bovine retinal pigment epithelium.
Authors: Christopher E Morgan / Zhemin Zhang / Masaru Miyagi / Marcin Golczak / Edward W Yu /
Abstract: The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on ...The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionMar 2, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26356.png

Downloads & links

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Map

FileDownload / File: emd_26356.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.8257036 - 2.9547527
Average (Standard dev.)7.2330346e-05 (±0.09443157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26356_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26356_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26356_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 : Decamer of Glutamine Synthetase

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

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Supramolecule #1: Decamer of Glutamine Synthetase

SupramoleculeName: Decamer of Glutamine Synthetase / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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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: cattle (cattle)
Molecular weightTheoretical: 42.085414 KDa
SequenceString: MATSASSHLN KGIKQVYMAL PQGDKVQAMY IWIDGTGEGL RCKTRTLDSE PKCIEELPEW NFDGSSTFQS EGSNSDMYLV PAAMFRDPF RKDPNKLVFC EVFKYNRKPA ETNLRHTCKR IMDMVSNQRP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String:
MATSASSHLN KGIKQVYMAL PQGDKVQAMY IWIDGTGEGL RCKTRTLDSE PKCIEELPEW NFDGSSTFQS EGSNSDMYLV PAAMFRDPF RKDPNKLVFC EVFKYNRKPA ETNLRHTCKR IMDMVSNQRP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD KAYGRDIVEA HYRACLYAGI KIGGTNAEVM PAQWEFQIGP CEGIDMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL KYIEEAIEKL SKRHQYHIRA YDPKGGLDNA RRLTGFHETS NINDFSAGVA NRG ASIRIP RTVGQEKKGY FEDRRPSANC DPFAVTEALI 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 stateparticle

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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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 58040
FSC plot (resolution estimation)

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