+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27630 | ||||||||||||
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Title | Structure of the PEAK3/14-3-3 complex | ||||||||||||
Map data | Reconstruction of the PEAK3/14-3-3 complex filtered to 3.1A and sharpened with 107.4 bFactor. | ||||||||||||
Sample |
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Keywords | complex / pseudokinase / kinase / adapter / SIGNALING PROTEIN | ||||||||||||
Function / homology | Function and homology information : / regulation of heart rate by hormone / : / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of toll-like receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...: / regulation of heart rate by hormone / : / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of toll-like receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / MTOR signalling / RAB GEFs exchange GTP for GDP on RABs / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of calcium ion export across plasma membrane / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of catalytic activity / Frs2-mediated activation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / protein kinase inhibitor activity / regulation of heart rate by cardiac conduction / regulation of mitotic cell cycle / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / protein localization to nucleus / phosphoserine residue binding / calcium channel regulator activity / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / HSF1 activation / potassium channel regulator activity / protein targeting / calcium channel inhibitor activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of cytosolic calcium ion concentration / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / substantia nigra development / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / hippocampus development / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / neuron migration / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / mitochondrial membrane / cerebral cortex development / histone deacetylase binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / Signaling by BRAF and RAF1 fusions / protein localization / actin cytoskeleton / melanosome / MHC class II protein complex binding / regulation of cell shape / cellular response to heat / protein phosphatase binding / scaffold protein binding / transmembrane transporter binding / protein kinase activity / intracellular signal transduction / cadherin binding / protein domain specific binding / protein heterodimerization activity / focal adhesion / ubiquitin protein ligase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / endoplasmic reticulum / RNA binding / extracellular exosome / identical protein binding / membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Torosyan H / Paul M / Jura N / Verba KA | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2023 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 | emd_27630.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-27630-v30.xml emd-27630.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27630_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_27630.png | 57.6 KB | ||
Masks | emd_27630_msk_1.map | 125 MB | Mask map | |
Others | emd_27630_half_map_1.map.gz emd_27630_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27630 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27630 | HTTPS FTP |
-Validation report
Summary document | emd_27630_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_27630_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_27630_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_27630_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27630 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27630 | HTTPS FTP |
-Related structure data
Related structure data | 8dp5MC 8ds6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27630.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Reconstruction of the PEAK3/14-3-3 complex filtered to 3.1A and sharpened with 107.4 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
File | emd_27630_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered, unsharpened half map.
File | emd_27630_half_map_1.map | ||||||||||||
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Annotation | Unfiltered, unsharpened half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered, unsharpened half map.
File | emd_27630_half_map_2.map | ||||||||||||
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Annotation | Unfiltered, unsharpened half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between PEAK3 and 14-3-3 epsilon, beta
Entire | Name: Complex between PEAK3 and 14-3-3 epsilon, beta |
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Components |
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-Supramolecule #1: Complex between PEAK3 and 14-3-3 epsilon, beta
Supramolecule | Name: Complex between PEAK3 and 14-3-3 epsilon, beta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 161.8 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: Homo sapiens (human) |
Molecular weight | Theoretical: 52.357031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
-Macromolecule #2: 14-3-3 protein beta/alpha
Macromolecule | Name: 14-3-3 protein beta/alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.114373 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTMDKSELVQ KAKLAEQAER YDDMAAAMKA VTEQGHELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TERNEKKQQM GKEYREKIE AELQDICNDV LELLDKYLIP NATQPESKVF YLKMKGDYFR YLSEVASGDN KQTTVSNSQQ AYQEAFEISK K EMQPTHPI ...String: MTMDKSELVQ KAKLAEQAER YDDMAAAMKA VTEQGHELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TERNEKKQQM GKEYREKIE AELQDICNDV LELLDKYLIP NATQPESKVF YLKMKGDYFR YLSEVASGDN KQTTVSNSQQ AYQEAFEISK K EMQPTHPI RLGLALNFSV FYYEILNSPE KACSLAKTAF DEAIAELDTL NEESYKDSTL IMQLLRDNLT LWTSENQGDE GD AGEGEN |
-Macromolecule #3: 14-3-3 protein epsilon
Macromolecule | Name: 14-3-3 protein epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.2089 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW RIISSIEQKE ENKGGEDKLK MIREYRQMV ETELKLICCD ILDVLDKHLI PAANTGESKV FYYKMKGDYH RYLAEFATGN DRKEAAENSL VAYKAASDIA M TELPPTHP ...String: MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW RIISSIEQKE ENKGGEDKLK MIREYRQMV ETELKLICCD ILDVLDKHLI PAANTGESKV FYYKMKGDYH RYLAEFATGN DRKEAAENSL VAYKAASDIA M TELPPTHP IRLGLALNFS VFYYEILNSP DRACRLAKAA FDDAIAELDT LSEESYKDST LIMQLLRDNL TLWTSDMQGD GE EQNKEAL QDVEDENQ |
-Macromolecule #4: Protein PEAK3 fragment
Macromolecule | Name: Protein PEAK3 fragment / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 52.437012 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSSPEPPTEP PEPDNPTWST QPTYSNLGQI RAHLLPSKAC RLRTPGSLST NPEPLPPPLP KKILTRTQ(SEP)L PTRRTL HPS SIQVQPPRRP FLGSHSVDKS QAAVGPACLP AELTFGPADA PLGLSLRDLH SPEAVHTALA ARQLQGLRTI YARLRAR LM GGHPGPCHPG ...String: MSSPEPPTEP PEPDNPTWST QPTYSNLGQI RAHLLPSKAC RLRTPGSLST NPEPLPPPLP KKILTRTQ(SEP)L PTRRTL HPS SIQVQPPRRP FLGSHSVDKS QAAVGPACLP AELTFGPADA PLGLSLRDLH SPEAVHTALA ARQLQGLRTI YARLRAR LM GGHPGPCHPG HSFRLLDSSP CAESGDALYY RVVRAHEDAW HILVAKVPKP GADVPHPWGL ELQASLSPHF NLQGLCGL V PEGTLPGAPW RGAVALAAEV PERTVAQWLA EACTQPPEEF VWAVALLLLQ LSAALKFLEA WGAALVELRP ENLLLVAPR GCATTGPPRL LLTDFGRVCL QPPGPPGSPG PHAPQLGSLL RALLSLAAPS TTPLAAGLEL LAAQLTRLRP SASRTRGALQ ALLWGPGPE LRGRGAPLGP WLRALGPWLR VRRGLLVLRL AERAAGGEAP SLEDWLCCEY LAEATESSMG QALALLWDLE G GGGADYKD DDDKGPV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-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: FIELD EMISSION GUN |
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 |