+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22650 | ||||||||||||||||||
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Title | Cryo-EM structure of STRIPAK complex | ||||||||||||||||||
Map data | SK7 primary map | ||||||||||||||||||
Sample |
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Keywords | phosphorylation / complex / PP2A / SIGNALING PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information FAR/SIN/STRIPAK complex / armadillo repeat domain binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex ...FAR/SIN/STRIPAK complex / armadillo repeat domain binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / negative regulation of intracellular estrogen receptor signaling pathway / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / : / positive regulation of microtubule binding / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / regulation of cell morphogenesis / regulation of Wnt signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / cortical actin cytoskeleton organization / negative regulation of glycolytic process through fructose-6-phosphate / Golgi cisterna membrane / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / regulation of DNA replication / mesoderm development / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of cell adhesion / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / cytoskeleton organization / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein dephosphorylation / RNA splicing / meiotic cell cycle / protein phosphatase 2A binding / response to organic substance / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / tau protein binding / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / small GTPase binding / kinase binding / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
Authors | Jeong B-C / Bai XC | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Cryo-EM structure of the Hippo signaling integrator human STRIPAK. Authors: Byung-Cheon Jeong / Sung Jun Bae / Lisheng Ni / Xuewu Zhang / Xiao-Chen Bai / Xuelian Luo / Abstract: The striatin-interacting phosphatase and kinase (STRIPAK) complex is a large, multisubunit protein phosphatase 2A (PP2A) assembly that integrates diverse cellular signals in the Hippo pathway to ...The striatin-interacting phosphatase and kinase (STRIPAK) complex is a large, multisubunit protein phosphatase 2A (PP2A) assembly that integrates diverse cellular signals in the Hippo pathway to regulate cell proliferation and survival. The architecture and assembly mechanism of this critical complex are poorly understood. Using cryo-EM, we determine the structure of the human STRIPAK core comprising PP2AA, PP2AC, STRN3, STRIP1, and MOB4 at 3.2-Å resolution. Unlike the canonical trimeric PP2A holoenzyme, STRIPAK contains four copies of STRN3 and one copy of each the PP2AA-C heterodimer, STRIP1, and MOB4. The STRN3 coiled-coil domains form an elongated homotetrameric scaffold that links the complex together. An inositol hexakisphosphate (IP) is identified as a structural cofactor of STRIP1. Mutations of key residues at subunit interfaces disrupt the integrity of STRIPAK, causing aberrant Hippo pathway activation. Thus, STRIPAK is established as a noncanonical PP2A complex with four copies of regulatory STRN3 for enhanced signal integration. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22650.map.gz | 166.2 MB | EMDB map data format | |
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Header (meta data) | emd-22650-v30.xml emd-22650.xml | 25.4 KB 25.4 KB | Display Display | EMDB header |
Images | emd_22650.png | 348.2 KB | ||
Filedesc metadata | emd-22650.cif.gz | 8.3 KB | ||
Others | emd_22650_additional_1.map.gz | 166.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22650 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22650 | HTTPS FTP |
-Related structure data
Related structure data | 7k36MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22650.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SK7 primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Focused map
File | emd_22650_additional_1.map | ||||||||||||
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Annotation | Focused map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SK7 complex
Entire | Name: SK7 complex |
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Components |
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-Supramolecule #1: SK7 complex
Supramolecule | Name: SK7 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 817.8 KDa |
-Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
Macromolecule | Name: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.378344 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ ...String: MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ YFRNLCSDDT PMVRRAAASK LGEFAKVLEL DNVKSEIIPM FSNLASDEQD SVRLLAVEAC VNIAQLLPQE DL EALVMPT LRQAAEDKSW RVRYMVADKF TELQKAVGPE ITKTDLVPAF QNLMKDCEAE VRAAASHKVK EFCENLSADC REN VIMSQI LPCIKELVSD ANQHVKSALA SVIMGLSPIL GKDNTIEHLL PLFLAQLKDE CPEVRLNIIS NLDCVNEVIG IRQL SQSLL PAIVELAEDA KWRVRLAIIE YMPLLAGQLG VEFFDEKLNS LCMAWLVDHV YAIREAATSN LKKLVEKFGK EWAHA TIIP KVLAMSGDPN YLHRMTTLFC INVLSEVCGQ DITTKHMLPT VLRMAGDPVA NVRFNVAKSL QKIGPILDNS TLQSEV KPI LEKLTQDQDV DVKYFAQEAL TVLSLA UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform |
-Macromolecule #2: Striatin-3
Macromolecule | Name: Striatin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 77.833484 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP QQYTIPGILH YIQHEWARFE MERAHWEVE RAELQARIAF LQGERKGQEN LKKDLVRRIK MLEYALKQER AKYHKLKYGT ELNQGDLKMP TFESEETKDT E APTAPQNS ...String: MDELAGGGGG GPGMAAPPRQ QQGPGGNLGL SPGGNGAAGG GGPPASEGAG PAAGPELSRP QQYTIPGILH YIQHEWARFE MERAHWEVE RAELQARIAF LQGERKGQEN LKKDLVRRIK MLEYALKQER AKYHKLKYGT ELNQGDLKMP TFESEETKDT E APTAPQNS QLTWKQGRQL LRQYLQEVGY TDTILDVRSQ RVRSLLGLSN SEPNGSVETK NLEQILNGGE SPKQKGQEIK RS SGDVLET FNFLENADDS DEDEENDMIE GIPEGKDKHR MNKHKIGNEG LAADLTDDPD TEEALKEFDF LVTAEDGEGA GEA RSSGDG TEWAEPITFP SGGGKSFIMG SDDVLLSVLG LGDLADLTVT NDADYSYDLP ANKDAFRKTW NPKYTLRSHF DGVR ALAFH PVEPVLVTAS EDHTLKLWNL QKTVPAKKSA SLDVEPIYTF RAHIGPVLSL AISSNGEQCF SGGIDATIQW WNMPS PSVD PYDTYEPNVL AGTLVGHTDA VWGLAYSGIK NQLLSCSADG TVRLWNPQEK LPCICTYNGD KKHGIPTSVD FIGCDP AHM VTSFNTGSAV IYDLETSQSL VILSSQVDSG LQSNNHINRV VSHPTLPVTI TAHEDRHIKF FDNKTGKMIH SMVAHLD AV TSLAVDPNGI YLMSGSHDCS IRLWNLDSKT CVQEITAHRK KLDESIYDVA FHSSKAYIAS AGADALAKVF V UniProtKB: Striatin-3 |
-Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
Macromolecule | Name: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.636152 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG ...String: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG GLSPSIDTLD HIRALDRLQE VPHEGPMCDL LWSDPDDRGG WGISPRGAGY TFGQDISETF NHANGLTLVS RA HQLVMEG YNWCHDRNVV TIFSAPNYCY RCGNQAAIME LDDTLKYSFL QFDPAPRRGE PHVTRRTPDY FL UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform |
-Macromolecule #4: MOB-like protein phocein
Macromolecule | Name: MOB-like protein phocein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.064447 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MVMAEGTAVL RRNRPGTKAQ DFYNWPDESF DEMDSTLAVQ QYIQQNIRAD CSNIDKILEP PEGQDEGVWK YEHLRQFCLE LNGLAVKLQ SECHPDTCTQ MTATEQWIFL CAAHKTPKEC PAIDYTRHTL DGAACLLNSN KYFPSRVSIK ESSVAKLGSV C RRIYRIFS ...String: MVMAEGTAVL RRNRPGTKAQ DFYNWPDESF DEMDSTLAVQ QYIQQNIRAD CSNIDKILEP PEGQDEGVWK YEHLRQFCLE LNGLAVKLQ SECHPDTCTQ MTATEQWIFL CAAHKTPKEC PAIDYTRHTL DGAACLLNSN KYFPSRVSIK ESSVAKLGSV C RRIYRIFS HAYFHHRQIF DEYENETFLC HRFTKFVMKY NLMSKDNLIV PILEEEVQNS VSGESEA UniProtKB: MOB-like protein phocein |
-Macromolecule #5: Striatin-interacting protein 1
Macromolecule | Name: Striatin-interacting protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 95.695656 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MEPAVGGPGP LIVNNKQPQP PPPPPPAAAQ PPPGAPRAAA GLLPGGKARE FNRNQRKDSE GYSESPDLEF EYADTDKWAA ELSELYSYT EGPEFLMNRK CFEEDFRIHV TDKKWTELDT NQHRTHAMRL LDGLEVTARE KRLKVARAIL YVAQGTFGEC S SEAEVQSW ...String: MEPAVGGPGP LIVNNKQPQP PPPPPPAAAQ PPPGAPRAAA GLLPGGKARE FNRNQRKDSE GYSESPDLEF EYADTDKWAA ELSELYSYT EGPEFLMNRK CFEEDFRIHV TDKKWTELDT NQHRTHAMRL LDGLEVTARE KRLKVARAIL YVAQGTFGEC S SEAEVQSW MRYNIFLLLE VGTFNALVEL LNMEIDNSAA CSSAVRKPAI SLADSTDLRV LLNIMYLIVE TVHQECEGDK AE WRTMRQT FRAELGSPLY NNEPFAIMLF GMVTKFCSGH APHFPMKKVL LLLWKTVLCT LGGFEELQSM KAEKRSILGL PPL PEDSIK VIRNMRAASP PASASDLIEQ QQKRGRREHK ALIKQDNLDA FNERDPYKAD DSREEEEEND DDNSLEGETF PLER DEVMP PPLQHPQTDR LTCPKGLPWA PKVREKDIEM FLESSRSKFI GYTLGSDTNT VVGLPRPIHE SIKTLKQHKY TSIAE VQAQ MEEEYLRSPL SGGEEEVEQV PAETLYQGLL PSLPQYMIAL LKILLAAAPT SKAKTDSINI LADVLPEEMP TTVLQS MKL GVDVNRHKEV IVKAISAVLL LLLKHFKLNH VYQFEYMAQH LVFANCIPLI LKFFNQNIMS YITAKNSISV LDYPHCV VH ELPELTAESL EAGDSNQFCW RNLFSCINLL RILNKLTKWK HSRTMMLVVF KSAPILKRAL KVKQAMMQLY VLKLLKVQ T KYLGRQWRKS NMKTMSAIYQ KVRHRLNDDW AYGNDLDARP WDFQAEECAL RANIERFNAR RYDRAHSNPD FLPVDNCLQ SVLGQRVDLP EDFQMNYDLW LEREVFSKPI SWEELLQ UniProtKB: Striatin-interacting protein 1 |
-Macromolecule #6: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #8: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was coated with gold prior to use | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 59524 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4356 / Average electron dose: 64.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2451582 |
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Startup model | Type of model: PDB ENTRY / Details: PDB ID 2NPP, 4N6J, 2YMU, 5YF4 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final 3D classification | Software - Name: RELION (ver. 3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 87779 |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL | ||||||||||
Output model | PDB-7k36: |