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- EMDB-51250: NME1 94-Diphosphoserine -

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Basic information

Entry
Database: EMDB / ID: EMD-51250
TitleNME1 94-Diphosphoserine
Map dataMain map, sharpened with DeepEMhancer
Sample
  • Complex: NME1, mutation T94S, di-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 / cytosol / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / 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: 3.3 Å
AuthorsRoderer D / Schoepf F / Fiedler D / Celik A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)469186007 Germany
CitationJournal: To Be Published
Title: Nucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation
Authors: Celif A / Schoepf F / Stieger CE / Morgan JAM / Lampe S / Ruwolt M / Liu F / Hackenberger CPR / Roderer D / Fiedler D
History
DepositionAug 5, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51250.png

Downloads & links

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Map

FileDownload / File: emd_51250.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
Contrast
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

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: 0.028
Minimum - Maximum-0.016520433 - 1.985576
Average (Standard dev.)0.0042097173 (±0.047989238)
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_51250_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened full map

Fileemd_51250_additional_1.map
AnnotationNon-sharpened full map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_51250_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_51250_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

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

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

SupramoleculeName: NME1, mutation T94S, di-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 / Number of copies: 6 / Enantiomer: LEVO / EC number: nucleoside-diphosphate kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.276732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHMAN CERTFIAIKP DGVQRGLVGE IIKRFEQKGF RLVGLKFMQA SEDLLKEHYV DLKDRPFFAG LVKYMHSGPV VAMVWEGLN VVKTGRVMLG E(DISEP)NPADSKPG TIRGDFCIQV GRNIIHGSDS VESAEKEIGL WFHPEELVDY TSCAQ NWIY E

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

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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: 4639 / Average exposure time: 2.0 sec. / Average electron dose: 44.6 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: 1.2 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: 1546555
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 486617
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: 168.57
Output model

PDB-9gd8:
NME1 94-Diphosphoserine

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