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- EMDB-68616: High-resolution cryo-EM structure of human Polo-like kinase 1 in ... -

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Entry
Database: EMDB / ID: EMD-68616
TitleHigh-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
Map data
Sample
  • Complex: High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
    • Protein or peptide: Serine/threonine-protein kinase PLK1
  • Ligand: 1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5,4-G]INDAZOLE-3-CARBOXAMIDE
Keywordssmall protein-ligand complex / TRANSFERASE
Function / homology
Function and homology information


positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly ...positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / astral microtubule organization / Golgi inheritance / outer kinetochore / mitotic cleavage furrow formation / microtubule bundle formation / mitotic chromosome condensation / double-strand break repair via alternative nonhomologous end joining / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / regulation of mitotic cell cycle phase transition / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / mitotic sister chromatid segregation / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / centriole / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / positive regulation of protein localization to nucleus / kinetochore / G2/M transition of mitotic cell cycle / spindle / centriolar satellite / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsPark K / Yoo Y / Jeon H / Choi K / Kwon E / Lim H / Kim DY / No KT
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: High-resolution cryo-EM structures of small protein-ligand complexes near the theoretical size limit.
Authors: Kunwoong Park / Youngki Yoo / Hyunbum Jeon / Kiju Choi / Hanseong Kim / Eunju Kwon / Hyun-Ho Lim / Dong Young Kim / Kyoung Tai No /
Abstract: Cryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM ...Cryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM structural analysis is estimated to be 38 kDa; typical constraints involve factors such as image contrast and particle alignment accuracy. In this study, we present cryo-EM structures of two protein-ligand complexes near this lower size threshold. First, the structure of the maltose-binding protein complexed with maltose, with a structurally ordered mass of 40.8 kDa, was determined at a resolution of 2.4 Å; both the maltose and water molecules were clearly identified in this structure. The second structure was the kinase domain of human PLK1 complexed with onvansertib, with a structurally ordered mass of 31.6 kDa, below the theoretical 38 kDa limit; this domain was determined at a resolution of 3.4 Å using a gold-supported grid in the presence of β-octyl-glucoside. The density map clearly shows the backbone of PLK1 secondary structure, and the onvansertib. These results demonstrate that cryo-EM can be effectively employed to determine structures of small proteins or domains, and to perform structure-based drug screening for small proteins, without requiring structural fiducials for particle alignment.
History
DepositionJan 21, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68616.png

Downloads & links

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Map

FileDownload / File: emd_68616.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 350 pix.
= 260.785 Å		0.75 Å/pix.
x 350 pix.
= 260.785 Å		0.75 Å/pix.
x 350 pix.
= 260.785 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7451 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.28876975 - 0.42290908
Average (Standard dev.)0.000013092852 (±0.00535289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 260.785 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68616_msk_1.map
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Half map: #1

Fileemd_68616_half_map_1.map
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Half map: #2

Fileemd_68616_half_map_2.map
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Sample components

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Entire : High-resolution cryo-EM structure of human Polo-like kinase 1 in ...

EntireName: High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
Components
  • Complex: High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
    • Protein or peptide: Serine/threonine-protein kinase PLK1
  • Ligand: 1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5,4-G]INDAZOLE-3-CARBOXAMIDE

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Supramolecule #1: High-resolution cryo-EM structure of human Polo-like kinase 1 in ...

SupramoleculeName: High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase PLK1

MacromoleculeName: Serine/threonine-protein kinase PLK1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.480621 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: APADPGKAGV PGVAAPGAPA AAPPAKEIPE VLVDPRSRRR YVRGRFLGKG GFAKCFEISD ADTKEVFAGK IVPKSLLLKP HQREKMSME ISIHRSLAHQ HVVGFHGFFE DNDFVFVVLE LCRRRSLLEL HKRRKALTEP EARYYLRQIV LGCQYLHRNR V IHRDLKLG ...String:
APADPGKAGV PGVAAPGAPA AAPPAKEIPE VLVDPRSRRR YVRGRFLGKG GFAKCFEISD ADTKEVFAGK IVPKSLLLKP HQREKMSME ISIHRSLAHQ HVVGFHGFFE DNDFVFVVLE LCRRRSLLEL HKRRKALTEP EARYYLRQIV LGCQYLHRNR V IHRDLKLG NLFLNEDLEV KIGDFGLATK VEYDGERKKV LCGTPNYIAP EVLSKKGHSF EVDVWSIGCI MYTLLVGKPP FE TSCLKET YLRIKKNEYS IPKHINPVAA SLIQKMLQTD PTARPTINEL LNDEFFTSGY IPARLPITCL TIPPRFSIAP SSL DPSNRK PLTVLNK

UniProtKB: Serine/threonine-protein kinase PLK1

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Macromolecule #2: 1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMET...

MacromoleculeName: 1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5,4-G]INDAZOLE-3-CARBOXAMIDE
type: ligand / ID: 2 / Number of copies: 1 / Formula: 937
Molecular weightTheoretical: 532.518 Da
Chemical component information

ChemComp-937:
1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5,4-G]INDAZOLE-3-CARBOXAMIDE

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6021153
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2yac

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200803
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2yac


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-22rd:
High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib

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