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- EMDB-64459: binary complex of polyP-bound polyphosphate kinase 1 (PPK1) -

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Basic information

Entry
Database: EMDB / ID: EMD-64459
Titlebinary complex of polyP-bound polyphosphate kinase 1 (PPK1)
Map data
Sample
  • Complex: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
    • Protein or peptide: Polyphosphate kinase
  • Ligand: Tetraphosphate
KeywordsCryoEM / Transferase
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
Polyphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsJiang WJ / Zhao J / Wei W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Insights into PPK1 Catalyzed Triple Phosphoryl Transfer Underlying Polyphosphate Biosynthesis
Authors: Jiang WJ / Zhao J / Wei W
History
DepositionApr 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64459.png

Downloads & links

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Map

FileDownload / File: emd_64459.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 297.2 Å		0.74 Å/pix.
x 400 pix.
= 297.2 Å		0.74 Å/pix.
x 400 pix.
= 297.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.621116 - 0.9416008
Average (Standard dev.)0.00058959407 (±0.028349511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 297.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64459_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64459_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64459_half_map_2.map
Projections & Slices
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Sample components

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Entire : binary complex of polyP-bound polyphosphate kinase 1 (PPK1)

EntireName: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
Components
  • Complex: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
    • Protein or peptide: Polyphosphate kinase
  • Ligand: Tetraphosphate

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Supramolecule #1: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)

SupramoleculeName: binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Polyphosphate kinase

MacromoleculeName: Polyphosphate kinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ATP-polyphosphate phosphotransferase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 80.01382 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EKLYIEKELS WLSFNERVLQ EAADKSNPLI ERMRFLGIYS NNLDEFYKVR FAELKRRIII SEEQGSNSHS RHLLGKIQSR VLKADQEFD GLYNELLLEM ARNQIFLINE RQLSVNQQNW LRHYFKQYLR QHITPILINP DTDLVQFLKD DYTYLAVEII R GDTIRYAL ...String:
EKLYIEKELS WLSFNERVLQ EAADKSNPLI ERMRFLGIYS NNLDEFYKVR FAELKRRIII SEEQGSNSHS RHLLGKIQSR VLKADQEFD GLYNELLLEM ARNQIFLINE RQLSVNQQNW LRHYFKQYLR QHITPILINP DTDLVQFLKD DYTYLAVEII R GDTIRYAL LEIPSDKVPR FVNLPPEAPR RRKPMILLDN ILRYCLDDIF KGFFDYDALN AYSMKMTRDA EYDLVHEMEA SL MELMSSS LKQRLTAEPV RFVYQRDMPN ALVEVLREKL TISRYDSIVP GGRYHNFKDF INFPNVGKAN LVNKPLPRLR HIW FDKAQF RNGFDAIRER DVLLYYPYHT FEHVLELLRQ ASFDPSVLAI KINIYRVAKD SRIIDSMIHA AHNGKKVTVV VELQ ARFDE EANIHWAKRL TEAGVHVIFS APGLKIHAKL FLISRKENGE VVRYAHIGTG NFNEKTARLY TDYSLLTADA RITNE VRRV FNFIENPYRP VTFDYLMVSP QNSRRLLYEM VDREIANAQQ GLPSGITLKL NNLVDKGLVD RLYAASSSGV PVNLLV AGM CSLIPNLEGI SDNIRAISIV DRYLEHDRVY IFENGGDKKV YLSSADWMTR NIDYRIEVAT PLLDPRLKQR VLDIIDI LF SDTVKARYID KELSNRYVPR GNRRKVRAQL AIYDYIKSLE QP

UniProtKB: Polyphosphate kinase

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Macromolecule #2: Tetraphosphate

MacromoleculeName: Tetraphosphate / type: ligand / ID: 2 / Number of copies: 4 / Formula: 7TT
Molecular weightTheoretical: 337.935 Da
Chemical component information

ChemComp-7TT:
Tetraphosphate

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER / Details: From cryoSPARC Ab-initio reconstrcution
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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