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- PDB-9urj: binary complex of polyP-bound polyphosphate kinase 1 (PPK1) -

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Basic information

Entry
Database: PDB / ID: 9urj
Titlebinary complex of polyP-bound polyphosphate kinase 1 (PPK1)
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / CryoEM
Function / homology
Function and homology information


diphosphotransferase activity / polyphosphate:AMP phosphotransferase activity / polyphosphate kinase complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / periplasmic side of cell outer membrane / polyphosphate kinase activity / phosphotransferase activity, phosphate group as acceptor / regulation of cell division / protein homodimerization activity ...diphosphotransferase activity / polyphosphate:AMP phosphotransferase activity / polyphosphate kinase complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / periplasmic side of cell outer membrane / polyphosphate kinase activity / phosphotransferase activity, phosphate group as acceptor / regulation of cell division / protein homodimerization activity / ATP binding / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 ...Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase C-terminal domain 1 / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
Tetraphosphate / Polyphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsJiang, W.J. / Zhao, J. / Wei, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Insights into PPK1 Catalyzed Triple Phosphoryl Transfer Underlying Polyphosphate Biosynthesis
Authors: Jiang, W.J. / Zhao, J. / Wei, W.
History
DepositionApr 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate kinase
B: Polyphosphate kinase
C: Polyphosphate kinase
D: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,4078
Polymers320,0554
Non-polymers1,3524
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
Polyphosphate kinase / ATP-polyphosphate phosphotransferase / Polyphosphoric acid kinase


Mass: 80013.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ppk, b2501, JW2486 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A7B1, ATP-polyphosphate phosphotransferase
#2: Chemical
ChemComp-7TT / Tetraphosphate / [oxidanyl(phosphonooxy)phosphoryl] phosphono hydrogen phosphate / [oxido-[oxido(phosphonatooxy)phosphoryl]oxyphosphoryl] phosphate


Mass: 337.935 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H6O13P4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38919 / Symmetry type: POINT

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