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- PDB-9gd8: NME1 94-Diphosphoserine -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9gd8
TitleNME1 94-Diphosphoserine
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / nucleotide kinase / post-translational modification / phosphorylation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRoderer, D. / Schoepf, F. / Fiedler, D. / Celik, A.
Funding support Germany, 1items
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, C.E. / Morgan, J.A.M. / Lampe, S. / Ruwolt, M. / Liu, F. / Hackenberger, C.P.R. / Roderer, D. / Fiedler, D.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
D: Nucleoside diphosphate kinase A
E: Nucleoside diphosphate kinase A
F: Nucleoside diphosphate kinase A


Theoretical massNumber of molelcules
Total (without water)109,6606
Polymers109,6606
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Nucleoside diphosphate kinase A / NDK A / NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23- ...NDK A / NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23-H1 / Tumor metastatic process-associated protein


Mass: 18276.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NME1, mutation T94S, di-phosphorylated at Ser94, Homo-hexamer
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 44.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4639
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU2.12image acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9cryoSPARC4.4.0initial Euler assignment
10cryoSPARC4.4.0final Euler assignment
11cryoSPARC4.4.0classification
12cryoSPARC4.4.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1546555
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 486617 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 168.57 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 9GD6

9gd6


Accession code: 9GD6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026786
ELECTRON MICROSCOPYf_angle_d0.4489150
ELECTRON MICROSCOPYf_dihedral_angle_d12.2172532
ELECTRON MICROSCOPYf_chiral_restr0.039972
ELECTRON MICROSCOPYf_plane_restr0.0021182

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