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- EMDB-51251: NME1 94-Oligophosphoserine -

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Basic information

Entry
Database: EMDB / ID: EMD-51251
TitleNME1 94-Oligophosphoserine
Map dataMain map, sharpened with DeepEMhancer
Sample
  • Complex: NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer
    • Protein or peptide: Nucleoside diphosphate kinase A
Keywordsnucleotide kinase / post-translational modification / phosphorylation / TRANSFERASE
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRoderer D / Schoepf F / Fiedler D / Celik A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)469186007 Germany
CitationJournal: Nat Chem / Year: 2025
Title: Nucleoside diphosphate kinase A (NME1) catalyses its own oligophosphorylation.
Authors: Arif Celik / Felix Schöpf / Christian E Stieger / Sarah Lampe / Björn Hanf / Jeremy A M Morgan / Max Ruwolt / Fan Liu / Christian P R Hackenberger / Daniel Roderer / Dorothea Fiedler /
Abstract: Protein phosphorylation is a central signalling mechanism in eukaryotic cells. The scope of this post-translational modification includes protein pyro- and polyphosphorylation. Here we report the ...Protein phosphorylation is a central signalling mechanism in eukaryotic cells. The scope of this post-translational modification includes protein pyro- and polyphosphorylation. Here we report the discovery of another mode of phosphorylation: protein oligophosphorylation. Using site-specifically phosphorylated and pyrophosphorylated nucleoside diphosphate kinase A (NME1), the effects of these modifications on enzyme activity were investigated. Phosphorylation, and more so pyrophosphorylation, on Thr94 reduced the nucleoside diphosphate kinase activity. Nevertheless, both phosphoprotein and pyrophosphoprotein catalysed their own oligophosphorylation-up to the formation of a hexaphosphate chain-using ATP as a cofactor. Oligophosphorylation was critically dependent on the catalytic histidine residue His118, and cryogenic electron microscopy analysis of the modified proteins suggests an intramolecular phosphoryl transfer mechanism. Oligophosphorylation of NME1 in biochemical samples, and in cell lysates, was further confirmed using mass spectrometry, and was found to promote a new set of protein interactions. Our results highlight the complex nature of phosphoregulation, and the methods described here provide the opportunity to investigate the impact of this unusual modification in the future.
History
DepositionAug 5, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51251.png

Downloads & links

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Map

FileDownload / File: emd_51251.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, sharpened with DeepEMhancer
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 192 pix.
= 159.36 Å		0.83 Å/pix.
x 192 pix.
= 159.36 Å		0.83 Å/pix.
x 192 pix.
= 159.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0016929663 - 1.9178157
Average (Standard dev.)0.0049255434 (±0.053878494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 159.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51251_msk_1.map
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Additional map: Non-sharpened map

Fileemd_51251_additional_1.map
AnnotationNon-sharpened map
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Half map: Half map 1

Fileemd_51251_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_51251_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer

EntireName: NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer
Components
  • Complex: NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer
    • Protein or peptide: Nucleoside diphosphate kinase A

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Supramolecule #1: NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer

SupramoleculeName: NME1, mutation T94S, tri-phosphorylated at Ser94, Homo-hexamer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nucleoside diphosphate kinase A

MacromoleculeName: Nucleoside diphosphate kinase A / type: protein_or_peptide / ID: 1
Details: NME1, mutant Thr94Ser, with triphosphorylation at Ser94
Number of copies: 6 / Enantiomer: LEVO / EC number: nucleoside-diphosphate kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.261525 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHMAN CERTFIAIKP DGVQRGLVGE IIKRFEQKGF RLVGLKFMQA SEDLLKEHYV DLKDRPFFAG LVKYMHSGPV VAMVWEGLN VVKTGRVMLG E(A1IKP)NPADSKPG TIRGDFCIQV GRNIIHGSDS VESAEKEIGL WFHPEELVDY T

UniProtKB: Nucleoside diphosphate kinase A

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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

Concentration0.9 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV
DetailsppS94-NME1 was incubated at 1 mM concentration with ATP for 3 h at 37 degrees celcius before vitrification.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4856 / Average exposure time: 2.0 sec. / Average electron dose: 44.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2121197
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ui4

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 201312
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9gd6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 229.16
Output model

PDB-9gd9:
NME1 94-Oligophosphoserine

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