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- EMDB-64511: binary complex of ATP-bound polyphosphate kinase 1 (PPK1) -

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Basic information

Entry
Database: EMDB / ID: EMD-64511
Titlebinary complex of ATP-bound polyphosphate kinase 1 (PPK1)
Map data
Sample
  • Complex: binary complex of ATP-bound polyphosphate kinase 1
    • Protein or peptide: Polyphosphate kinase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCryo-EM / wild type PPK1 / TRANSFERASE
Function / homology
Function and homology information


polyphosphate kinase complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / polyphosphate kinase activity / ATP binding / metal ion binding
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 speciesHomo sapiens (human) / Citrobacter freundii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 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
DepositionMay 7, 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_64511.png

Downloads & links

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Map

FileDownload / File: emd_64511.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.)
0.82 Å/pix.
x 400 pix.
= 327.6 Å		0.82 Å/pix.
x 400 pix.
= 327.6 Å		0.82 Å/pix.
x 400 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.161
Minimum - Maximum-0.5162446 - 0.980053
Average (Standard dev.)0.0009484273 (±0.026346141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64511_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: #1

Fileemd_64511_half_map_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_64511_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : binary complex of ATP-bound polyphosphate kinase 1

EntireName: binary complex of ATP-bound polyphosphate kinase 1
Components
  • Complex: binary complex of ATP-bound polyphosphate kinase 1
    • Protein or peptide: Polyphosphate kinase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: binary complex of ATP-bound polyphosphate kinase 1

SupramoleculeName: binary complex of ATP-bound polyphosphate kinase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: Citrobacter freundii (bacteria)
Molecular weightTheoretical: 80.015742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KLYIEKELSW LAFNERVLQE AADKSNPLIE RMRFLGIYSN NLDEFYKVRF AELKRRIIIS EEQGSNSHSR HLLGKIQARV LKADQEFDG LYNELLLEMA RNQIFLINER QLSANQQSWL RHYFKQYLRQ HITPILINRE TDLVQFLKDD YTYLAVEIIR G DTIRYALL ...String:
KLYIEKELSW LAFNERVLQE AADKSNPLIE RMRFLGIYSN NLDEFYKVRF AELKRRIIIS EEQGSNSHSR HLLGKIQARV LKADQEFDG LYNELLLEMA RNQIFLINER QLSANQQSWL RHYFKQYLRQ HITPILINRE TDLVQFLKDD YTYLAVEIIR G DTIRYALL EIPSDKVPRF VNLPPETPRR RKPMILLDNI LRYCLDDIFK GFFDYDALNA YSMKMTRDAE YDLVHEMESS LM ELMSSSL KQRLTAEPVR FVYQRDMPNA LVEVLREKLT ISRYDSIVPG GRYHNFKDFI NFPNVGKANL VNKPLPRLRH IWF DNEKFR NGFDAIRERD VLLYYPYHTF EHVLELLRQA SFDPSVLAIK INIYRVAKDS RIIDAMIHAA HNSKKVTVVV ELQA RFDEE ANIHWAKRLT EAGVHVIFSA PGLKIHAKLF LISRKEGDEV VRYAHIGTGN FNEKTARLYT DYSLLTADSR ITNEV RRVF NFIENPYRPV TFDYLLVSPQ NSRRLLYAMI DKEIANAQQG QPSGITLKLN NLVDKGLVDR LYAASSSGVP VNLLIR GMC SLIPNLEGIS DNIRVISIVD RYLEHDRVYI FENGGDKQVY LSSADWMTRN IDYRIEVATP LLDPRLKQRV LDIIDIL FS DTVKARFIDK ELSNRYVPRG NRRKVQSQLA IYDYIKSLEQ P

UniProtKB: Polyphosphate kinase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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 AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: From Ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55294
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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