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- EMDB-42892: Composite map of AMPylated GlnA bound to hinT -

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Basic information

Entry
Database: EMDB / ID: EMD-42892
TitleComposite map of AMPylated GlnA bound to hinT
Map datacomposite map of GlnA dimer bound with hinT dimer
Sample
  • Complex: GlnA dimer binding to hinT dimer
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: Purine nucleoside phosphoramidase
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsAMPylation / adenyltransferase / nucleotide binding protein / LIGASE-HYDROLASE complex
Function / homology
Function and homology information


ammonia assimilation cycle / D-alanine catabolic process / nitrogen utilization / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / nucleotide binding ...ammonia assimilation cycle / D-alanine catabolic process / nitrogen utilization / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / nucleotide binding / protein homodimerization activity / 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 / Histidine triad (HIT) protein / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / HIT domain / Glutamine synthetase putative ATP-binding region signature. ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Histidine triad (HIT) protein / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / HIT domain / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Histidine triad, conserved site / HIT domain signature. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / HIT domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / HIT-like domain / HIT-like superfamily / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase / Purine nucleoside phosphoramidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_42892.png

Downloads & links

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Map

FileDownload / File: emd_42892.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of GlnA dimer bound with hinT dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 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: 0.15
Minimum - Maximum-0.0017751936 - 3.7284288
Average (Standard dev.)0.0017740608 (±0.03107112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GlnA dimer binding to hinT dimer

EntireName: GlnA dimer binding to hinT dimer
Components
  • Complex: GlnA dimer binding to hinT dimer
    • Protein or peptide: Glutamine synthetase
    • Protein or peptide: Purine nucleoside phosphoramidase
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: GlnA dimer binding to hinT dimer

SupramoleculeName: GlnA dimer binding to hinT dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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: Purine nucleoside phosphoramidase

MacromoleculeName: Purine nucleoside phosphoramidase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on phosphorus-nitrogen bonds
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.637674 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMGSMAEET IFSKIIRREI PSDIVYQDDL VTAFRDISPQ APTHILIIPN ILIPTVNDVS AEHEQALGRM ITVAAKIAEQ EGIAEDGYR LIMNTNRHGG QEVYHINMHL LGGRPLGPML AHKGL

UniProtKB: Purine nucleoside phosphoramidase

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Macromolecule #3: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 225422
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8v1y:
Composite map of AMPylated GlnA bound to hinT

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