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Yorodumi- EMDB-44552: Septin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44552 | ||||||||||||
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Title | Septin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis by Cryo-EM | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Complex / SPA / Cytoskeleton / Septin / CELL CYCLE | ||||||||||||
Function / homology | Function and homology information septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / cilium assembly / cilium / kinetochore / microtubule cytoskeleton / protein localization ...septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / cilium assembly / cilium / kinetochore / microtubule cytoskeleton / protein localization / molecular adaptor activity / GTPase activity / GTP binding Similarity search - Function | ||||||||||||
Biological species | Ciona intestinalis (vase tunicate) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||
Authors | Mendonca DC / Pereira HM / Garratt RC | ||||||||||||
Funding support | Brazil, 3 items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Structural Insights into Ciona intestinalis Septins: Complexes Suggest a Mechanism for Nucleotide-dependent Interfacial Cross-talk. Authors: Deborah C Mendonça / Sinara T B Morais / Heloísa Ciol / Andressa P A Pinto / Diego A Leonardo / Humberto D'Muniz Pereira / Napoleão F Valadares / Rodrigo V Portugal / Bruno P Klaholz / ...Authors: Deborah C Mendonça / Sinara T B Morais / Heloísa Ciol / Andressa P A Pinto / Diego A Leonardo / Humberto D'Muniz Pereira / Napoleão F Valadares / Rodrigo V Portugal / Bruno P Klaholz / Richard C Garratt / Ana P U Araujo / Abstract: Septins are filamentous nucleotide-binding proteins which can associate with membranes in a curvature-dependent manner leading to structural remodelling and barrier formation. Ciona intestinalis, a ...Septins are filamentous nucleotide-binding proteins which can associate with membranes in a curvature-dependent manner leading to structural remodelling and barrier formation. Ciona intestinalis, a model for exploring the development and evolution of the chordate lineage, has only four septin-coding genes within its genome. These represent orthologues of the four classical mammalian subgroups, making it a minimalist non-redundant model for studying the modular assembly of septins into linear oligomers and thereby filamentous polymers. Here, we show that C. intestinalis septins present a similar biochemistry to their human orthologues and also provide the cryo-EM structures of an octamer, a hexamer and a tetrameric sub-complex. The octamer, which has the canonical arrangement (2-6-7-9-9-7-6-2) clearly shows an exposed NC-interface at its termini enabling copolymerization with hexamers into mixed filaments. Indeed, only combinations of septins which had CiSEPT2 occupying the terminal position were able to assemble into filaments via NC-interface association. The CiSEPT7-CiSEPT9 tetramer is the smallest septin particle to be solved by Cryo-EM to date and its good resolution (2.7 Å) provides a well-defined view of the central NC-interface. On the other hand, the CiSEPT7-CiSEPT9 G-interface shows signs of fragility permitting toggling between hexamers and octamers, similar to that seen in human septins but not in yeast. The new structures provide insights concerning the molecular mechanism for cross-talk between adjacent interfaces. This indicates that C. intestinalis may represent a valuable tool for future studies, fulfilling the requirements of a complete but simpler system to understand the mechanisms behind the assembly and dynamics of septin filaments. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44552.map.gz | 254.1 MB | EMDB map data format | |
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Header (meta data) | emd-44552-v30.xml emd-44552.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44552_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_44552.png | 58.6 KB | ||
Masks | emd_44552_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-44552.cif.gz | 6.3 KB | ||
Others | emd_44552_additional_1.map.gz emd_44552_additional_2.map.gz emd_44552_half_map_1.map.gz emd_44552_half_map_2.map.gz | 483.4 MB 449 MB 475.2 MB 475.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44552 | HTTPS FTP |
-Validation report
Summary document | emd_44552_validation.pdf.gz | 721 KB | Display | EMDB validaton report |
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Full document | emd_44552_full_validation.pdf.gz | 720.6 KB | Display | |
Data in XML | emd_44552_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_44552_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44552 | HTTPS FTP |
-Related structure data
Related structure data | 9bhtMC 9bhwC 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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-Map
File | Download / File: emd_44552.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.862 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_44552_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Sharppened map
File | emd_44552_additional_1.map | ||||||||||||
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Annotation | Sharppened map | ||||||||||||
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Density Histograms |
-Additional map: DeepEMhancer map
File | emd_44552_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_44552_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44552_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
Entire | Name: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7 |
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Components |
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-Supramolecule #1: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
Supramolecule | Name: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Ciona intestinalis (vase tunicate) |
-Macromolecule #1: CiSeptin-2
Macromolecule | Name: CiSeptin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Ciona intestinalis (vase tunicate) |
Molecular weight | Theoretical: 50.766543 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMEKHQL ERHRSIRKNA RIVSHFSPDP KYNPSEIRKK YEGYTSPASK EREEQVKFK FTNPETPGYV GFANLPNQVH RKSVKKGFEF TLMVAGESGL GKSTLVNSLF LTDLYPERCI PPAADKITQT V KIDASTVE ...String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMEKHQL ERHRSIRKNA RIVSHFSPDP KYNPSEIRKK YEGYTSPASK EREEQVKFK FTNPETPGYV GFANLPNQVH RKSVKKGFEF TLMVAGESGL GKSTLVNSLF LTDLYPERCI PPAADKITQT V KIDASTVE IEERGVKLRL TVVDTPGYGD AINCSDCYKP IIQYIDDQFE RYLHDESGLN RRHIVDNRVH SCFYFISSQG HG LKPLDIE FMKALHNKVN IVPVLSKADS LTMPEVKRLK RRILEEIAAH EIQIYQLPDA DEDEDEEFKE QTRCLKESIP FAV VGSTQM IEVKGKKVRG RLYPWGVVEV ENPDHCDFLK LRTMLITHMQ DLQEVTHDLH YENFRARRLQ SKDGEPANVS VDSG SNNRA LQEKEAELQR MQEMVQQMQA QIKAQSKSSP TGSKVVSHQI |
-Macromolecule #2: CiSeptin-6
Macromolecule | Name: CiSeptin-6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Ciona intestinalis (vase tunicate) |
Molecular weight | Theoretical: 49.661637 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVKMEKDEAA GDYNGSVDEG MRTLNLSGHV GFDSLPDQLV NKATNQGFCF NILCIGETGL GKSTLMNTLF NTNFENEPQH HNMPGVKLK ANTYELQESN VRLKLTIVDS VGFGDQINKE ESFKPVVEYI NQQFENYLQE ELKICRSLFS YHDTRIHACL Y FISPTGHG ...String: MVKMEKDEAA GDYNGSVDEG MRTLNLSGHV GFDSLPDQLV NKATNQGFCF NILCIGETGL GKSTLMNTLF NTNFENEPQH HNMPGVKLK ANTYELQESN VRLKLTIVDS VGFGDQINKE ESFKPVVEYI NQQFENYLQE ELKICRSLFS YHDTRIHACL Y FISPTGHG LKSLDLKTMK NLDNKVNIIP VIAKADIVSK GELHKFKIKI MNELVTNGVQ IYQFPTDDET VAEVNASMNT HL PFAVVGS TEEIKLGNKM VKARQYPWGT VQVENENHCD FVKLREMLVR VNMEDLREKT HTKHYELYRR SKLTEMGFID DND GGKNFS LQEVYESKRN DHLNELQRKE DEMRQMFVLR VKDKEGELKK SEKELHDKFD KLKKMHMEEK KKLEEKKKSL QDEI TGFEK KRQQAETLGK EHLAMSQNKT GKKK UniProtKB: Septin |
-Macromolecule #3: CiSeptin-7
Macromolecule | Name: CiSeptin-7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Ciona intestinalis (vase tunicate) |
Molecular weight | Theoretical: 48.769039 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVLLNQDMAQ QPKALDSYVG FANLPNQLYR KSVKQGFEFT LMVVGESGLG KSTLINSLFL SDLYSNEYPG PSLRIKKTVK VETTKVLIK ENGVTLRLTI DDTPGFGDAV DNSNCWQAVI NHIEKKFEDY LNAESMVTRS KLADNRVHCC LYFIAPTGHG L KPLDVEFM ...String: MVLLNQDMAQ QPKALDSYVG FANLPNQLYR KSVKQGFEFT LMVVGESGLG KSTLINSLFL SDLYSNEYPG PSLRIKKTVK VETTKVLIK ENGVTLRLTI DDTPGFGDAV DNSNCWQAVI NHIEKKFEDY LNAESMVTRS KLADNRVHCC LYFIAPTGHG L KPLDVEFM KNLHDKVNII PLIAKADTMT PEECLRFKKQ IMKEIHEHKI QLYEFPECED EEENRLNRKL KSRVPFAVVG SN TVLEIGG RRVRGRQYPW GVAEVENIDH CDFTVLRNML VRTHMQDLKD VTNNVHYENY RSKKLSSVTT TTMDGRSKAQ TKS PLAQME EEKSEHMQKM KKMEMEEVFR MKVHEKKQKL QESEADLSRR HEAMKKKLEA EYAALDEKQR QYEKDKQDFE ALQL KLMED RKSDNRTLGR KKKW UniProtKB: Septin |
-Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.3 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: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |