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Open data
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Basic information
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Title | Structure of the PEAK3 pseudokinase homodimer | ||||||||||||
![]() | Reconstruction of the PEAK3 pseudokinase homodimer filtered to 4.9A and sharpened with -105 bFactor. | ||||||||||||
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![]() | complex / pseudokinase / kinase / adapter / SIGNALING PROTEIN | ||||||||||||
Function / homology | : / regulation of actin cytoskeleton organization / actin cytoskeleton / regulation of cell shape / protein kinase activity / focal adhesion / Protein PEAK3![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||
![]() | Torosyan H / Paul M / Jura N / Verba KA | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Authors: Hayarpi Torosyan / Michael D Paul / Antoine Forget / Megan Lo / Devan Diwanji / Krzysztof Pawłowski / Nevan J Krogan / Natalia Jura / Kliment A Verba / ![]() ![]() Abstract: PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK ...PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 60.1 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 98.3 MB 98.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ds6MC ![]() 8dp5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of the PEAK3 pseudokinase homodimer filtered to 4.9A and sharpened with -105 bFactor. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: unfiltered, unsharpened half maps
File | emd_27684_half_map_1.map | ||||||||||||
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Annotation | unfiltered, unsharpened half maps | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered, unsharpened half maps
File | emd_27684_half_map_2.map | ||||||||||||
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Annotation | unfiltered, unsharpened half maps | ||||||||||||
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Density Histograms |
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Sample components
-Entire : PEAK3 pseudokinase homodimer
Entire | Name: PEAK3 pseudokinase homodimer |
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Components |
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-Supramolecule #1: PEAK3 pseudokinase homodimer
Supramolecule | Name: PEAK3 pseudokinase homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 104.58 KDa |
-Macromolecule #1: Protein PEAK3
Macromolecule | Name: Protein PEAK3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 52.357031 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSSPEPPTEP PEPDNPTWST QPTYSNLGQI RAHLLPSKAC RLRTPGSLST NPEPLPPPLP KKILTRTQSL PTRRTLHPSS IQVQPPRRP FLGSHSVDKS QAAVGPACLP AELTFGPADA PLGLSLRDLH SPEAVHTALA ARQLQGLRTI YARLRARLMG G HPGPCHPG ...String: MSSPEPPTEP PEPDNPTWST QPTYSNLGQI RAHLLPSKAC RLRTPGSLST NPEPLPPPLP KKILTRTQSL PTRRTLHPSS IQVQPPRRP FLGSHSVDKS QAAVGPACLP AELTFGPADA PLGLSLRDLH SPEAVHTALA ARQLQGLRTI YARLRARLMG G HPGPCHPG HSFRLLDSSP CAESGDALYY RVVRAHEDAW HILVAKVPKP GADVPHPWGL ELQASLSPHF NLQGLCGLVP EG TLPGAPW RGAVALAAEV PERTVAQWLA EACTQPPEEF VWAVALLLLQ LSAALKFLEA WGAALVELRP ENLLLVAPRG CAT TGPPRL LLTDFGRVCL QPPGPPGSPG PHAPQLGSLL RALLSLAAPS TTPLAAGLEL LAAQLTRLRP SASRTRGALQ ALLW GPGPE LRGRGAPLGP WLRALGPWLR VRRGLLVLRL AERAAGGEAP SLEDWLCCEY LAEATESSMG QALALLWDLE GGGGA DYKD DDDKGPV UniProtKB: Protein PEAK3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: A final concentration of 0.1% of Octyl-beta-Glucoside (C14H28O6) was added to the sample before freezing. | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot time = 7s blot force = 4. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 69.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |