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- EMDB-55334: CryoEM structure of nucleoside diphosphate kinase (NDK) dodecamer... -

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Basic information

Entry
Database: EMDB / ID: EMD-55334
TitleCryoEM structure of nucleoside diphosphate kinase (NDK) dodecamer 1 from Streptococcus pneumoniae
Map dataFull map of NDK dodecamere 1
Sample
  • Complex: Dodecameric form of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
    • Protein or peptide: Nucleoside diphosphate kinase
Keywordskinase / dodecamer / soluble protein / TRANSFERASE
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
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
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.09 Å
AuthorsNouri P / Kerboeuf J / Giraud M-F / Lambert O / Daury L / Kaplan E / Jault J-M / Gonzalez C
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Protein Sci / Year: 2026
Title: Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies.
Authors: Julie Kerboeuf / Paul Nouri / Frédéric Galisson / Laetitia Daury / Marie-France Giraud / Olivier Lambert / Cédric Orelle / Lionel Ballut / Elise Kaplan / Jean-Michel Jault / Cécile Gonzalez /
Abstract: The nucleoside diphosphate kinase (NDK) is a key enzyme that controls the balance of nucleotide pools in all living organisms. Beyond this fundamental role, NDKs exert pleiotropic effects in many ...The nucleoside diphosphate kinase (NDK) is a key enzyme that controls the balance of nucleotide pools in all living organisms. Beyond this fundamental role, NDKs exert pleiotropic effects in many cellular processes, including cell development, signal transduction, differentiation, tumor metastasis, and gene expression. The quaternary structure of NDK is typically hexameric-organized as a trimer of dimers in eukaryotic cells and in many prokaryotes-though in some species it can also be tetrameric. Here, we report the crystal structure of Streptococcus pneumoniae NDK (SpNDK) in its apo state (1.2 Å) and in an adenosine diPhosphate (ADP)-vanadate-bound state (3.4 Å). In both structures, SpNDK adopts a hexameric assembly and the fold of each monomer is highly conserved compared to NDKs from other organisms. A notable feature is the extended Kpn-loop, which plays a key role in stabilizing the hexamer. The protein exhibited remarkably high thermal stability (T ~ 76°C). However, mutation of R28 (R28A), which interacts with the Kpn-loop, destabilized the hexamer, lowering the T by >20°C. Unexpectedly, size-exclusion chromatography and mass photometry revealed that wild-type SpNDK exists as an equilibrium mixture of hexamers, dodecamers, and higher-order supramolecular assemblies. Using cryo-electron microscopy, we solved the three Dimensional (3D) structure of the hexameric state at 2.47 Å resolution, and resolved dodecameric assemblies of the protein. Since the oligomeric state of the NDK influences its cellular function, further investigations will be needed to address the in vivo relevance of these findings, in line with the broad and multifaceted roles of this enzyme family.
History
DepositionOct 8, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55334.png

Downloads & links

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Map

FileDownload / File: emd_55334.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of NDK dodecamere 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 384 pix.
= 266.496 Å		0.69 Å/pix.
x 384 pix.
= 266.496 Å		0.69 Å/pix.
x 384 pix.
= 266.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.694 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0215
Minimum - Maximum-0.08765398 - 0.19445367
Average (Standard dev.)0.000018371276 (±0.0046357876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 266.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of NDK dodecamere 1

Fileemd_55334_half_map_1.map
AnnotationHalf map A of NDK dodecamere 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of NDK dodecamere 1

Fileemd_55334_half_map_2.map
AnnotationHalf map B of NDK dodecamere 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 : Dodecameric form of nucleoside diphosphate kinase (NDK) from Stre...

EntireName: Dodecameric form of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
Components
  • Complex: Dodecameric form of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
    • Protein or peptide: Nucleoside diphosphate kinase

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Supramolecule #1: Dodecameric form of nucleoside diphosphate kinase (NDK) from Stre...

SupramoleculeName: Dodecameric form of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae R6 (bacteria)

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Macromolecule #1: Nucleoside diphosphate kinase

MacromoleculeName: Nucleoside diphosphate kinase / type: protein_or_peptide / ID: 1 / Details: dodecamer, soluble protein kinase, Transferase / Enantiomer: LEVO / EC number: nucleoside-diphosphate kinase
Source (natural)Organism: Streptococcus pneumoniae R6 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MEQTFFIIKP DGVKRGLVGE VLKRIEQRGF TIEKLEFRSQ VSEELIDQHY QDLVGQSFYP PIREFMTSG PVLVGVISGP KVIETWRTMM GATRPEEALP GTIRGDFAKA AGENEIIQNV VHGSDSEESA KREIALWF

UniProtKB: Nucleoside diphosphate kinase

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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

Concentration0.25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
50.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid

Details: 50 mM Hepes pH 7.4, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3184 / Average exposure time: 3.69 sec. / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1653163
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 62236
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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