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- EMDB-42896: GlnA dodecamer with AMPylation -

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Basic information

Entry
Database: EMDB / ID: EMD-42896
TitleGlnA dodecamer with AMPylation
Map datamap of GlnA dodecamer
Sample
  • Complex: GlnA dodecamer
    • Protein or peptide: Glutamine synthetase
  • Ligand: MANGANESE (II) ION
KeywordsAMPylation / adenyltransferase / LIGASE
Function / homology
Function and homology information


ammonia assimilation cycle / nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / ATP binding / metal ion binding / identical protein binding / membrane ...ammonia assimilation cycle / nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / ATP binding / metal ion binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / 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 class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / 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 speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsHan Y / Sreelatha A / Gonzalez A / Chen Z
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK123194 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR190106 United States
Welch FoundationI-2046-20200401 United States
Welch FoundationI-2046-20230405 United States
CitationJournal: Nat Commun / Year: 2025
Title: A repurposed AMP binding domain reveals mitochondrial protein AMPylation as a regulator of cellular metabolism.
Authors: Abner Gonzalez / Alex Pon / Kelly Servage / Krzysztof Pawłowski / Yan Han / Anju Sreelatha /
Abstract: Protein AMPylation, the covalent addition of adenosine monophosphate (AMP) to protein substrates, has been known as a post translational modification for over 50 years. Research in this field is ...Protein AMPylation, the covalent addition of adenosine monophosphate (AMP) to protein substrates, has been known as a post translational modification for over 50 years. Research in this field is largely underdeveloped due to the lack of tools that enable the systematic identification of AMPylated substrates. Here, we address this gap by developing an enrichment technique to isolate and study AMPylated proteins using a nucleotide-binding protein, hinT. Cryo-EM reconstruction of an AMPylated protein bound to hinT provides a structural basis for AMP selectivity. Using structure guided mutagenesis, we optimize enrichment to identify novel substrates of the evolutionarily conserved AMPylase, Selenoprotein O. We show that mammalian Selenoprotein O regulates metabolic flux through AMPylation of key mitochondrial proteins including glutamate dehydrogenase and pyruvate dehydrogenase. Our findings highlight the broader significance of AMPylation, an emerging post translational modification with critical roles in signal transduction and disease pathology. Furthermore, we establish a powerful enrichment platform for the discovery of novel AMPylated proteins to study the mechanisms and significance of protein AMPylation in cellular function.
History
DepositionNov 21, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42896.png

Downloads & links

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Map

FileDownload / File: emd_42896.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of GlnA dodecamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0017693884 - 1.4441371
Average (Standard dev.)0.0031497565 (±0.03896282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1 of GlnA dodecamer

Fileemd_42896_half_map_1.map
Annotationhalf map 1 of GlnA dodecamer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of GlnA dodecamer

Fileemd_42896_half_map_2.map
Annotationhalf map 2 of GlnA dodecamer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GlnA dodecamer

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

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Supramolecule #1: GlnA dodecamer

SupramoleculeName: GlnA dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.57225 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SEFELMSAEH VLTMLNEHEV KFVDLRFTDT KGKEQHVTIP AHQVNAEFFE EGKMFDGSSI GGWKGINESD MVLMPDASTA VIDPFFADS TLIIRCDILE PGTLQGYDRD PRSIAKRAED YLRSTGIADT VLFGPEPEFF LFDDIRFGSS ISGSHVAIDD I EGAWNSST ...String:
SEFELMSAEH VLTMLNEHEV KFVDLRFTDT KGKEQHVTIP AHQVNAEFFE EGKMFDGSSI GGWKGINESD MVLMPDASTA VIDPFFADS TLIIRCDILE PGTLQGYDRD PRSIAKRAED YLRSTGIADT VLFGPEPEFF LFDDIRFGSS ISGSHVAIDD I EGAWNSST QYEGGNKGHR PAVKGGYFPV PPVDSAQDIR SEMCLVMEQM GLVVEAHHHE VATAGQNEVA TRFNTMTKKA DE IQIYKYV VHNVAHRFGK TATFMPKPMF GDNGSGMHCH MSLSKNGVNL FAGDKYAGLS EQALYYIGGV IKHAKAINAL ANP TTNSYK RLVPGYEAPV MLAYSARNRS ASIRIPVVSS PKARRIEVRF PDPAANPYLC FAALLMAGLD GIKNKIHPGE AMDK NLYDL PPEEAKEIPQ VAGSLEEALN ELDLDREFLK AGGVFTDEAI DAYIALRREE DDRVRMTPHP VEFELYYSV

UniProtKB: Glutamine synthetase

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 12 / 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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: relion ab initio model
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 495703
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8v22:
GlnA dodecamer with AMPylation

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