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- EMDB-44555: Septin Tetrameric Complex SEPT7/SEPT9 of Ciona intestinalis by Cryo-EM -

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Basic information

Entry
Database: EMDB / ID: EMD-44555
TitleSeptin Tetrameric Complex SEPT7/SEPT9 of Ciona intestinalis by Cryo-EM
Map dataRaw map
Sample
  • Complex: Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9
    • Protein or peptide: CiSeptin-7
    • Protein or peptide: Neuronal-specific septin-3
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsComplex / SPA / Cytoskeleton / CELL CYCLE
Function / homology
Function and homology information


septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / kinetochore / spindle / intracellular protein localization / microtubule cytoskeleton / midbody ...septin complex / septin ring / cytoskeleton-dependent cytokinesis / cell division site / cleavage furrow / kinetochore / spindle / intracellular protein localization / microtubule cytoskeleton / midbody / molecular adaptor activity / cilium / GTPase activity / GTP binding
Similarity search - Function
Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Neuronal-specific septin-3 / Septin
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsMendonca DC / Pereira HM / Garratt RC
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/20209-5 Brazil
Sao Paulo Research Foundation (FAPESP)2020/02897-1 Brazil
Sao Paulo Research Foundation (FAPESP)2023/06866-1 Brazil
CitationJournal: 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
DepositionApr 22, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44555.png

Downloads & links

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Map

FileDownload / File: emd_44555.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å		0.73 Å/pix.
x 480 pix.
= 349.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2115823 - 0.4734393
Average (Standard dev.)-0.00019642853 (±0.0073344978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 349.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44555_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Additional map: Sharpened map

Fileemd_44555_additional_1.map
AnnotationSharpened map
Projections & Slices
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Additional map: DeepEMhancer map

Fileemd_44555_additional_2.map
AnnotationDeepEMhancer map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_44555_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_44555_half_map_2.map
AnnotationHalf map B
Projections & Slices
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Sample components

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Entire : Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9

EntireName: Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9
Components
  • Complex: Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9
    • Protein or peptide: CiSeptin-7
    • Protein or peptide: Neuronal-specific septin-3
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9

SupramoleculeName: Ciona intestinalis Septin Tetrameric Complex SEPT7/SEPT9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ciona intestinalis (vase tunicate)

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Macromolecule #1: CiSeptin-7

MacromoleculeName: CiSeptin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ciona intestinalis (vase tunicate)
Molecular weightTheoretical: 48.769039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: Neuronal-specific septin-3

MacromoleculeName: Neuronal-specific septin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ciona intestinalis (vase tunicate)
Molecular weightTheoretical: 41.559363 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTTPLEGYVG IDTLTEQIRK KALRQGFEFN VMVVGSAGLG KSTLVNTIFK SKVSRRQPEE DYHTPSTVEI KTISHVIEEK GILLKLSVT DTPGFGDQVD NTNCWQPIMR HVNEQYEKYL NEEISIKRRK RIPDTRVHCC IYFIPPSGHS LRLVDIEVMK R LVEIVNVI ...String:
MTTPLEGYVG IDTLTEQIRK KALRQGFEFN VMVVGSAGLG KSTLVNTIFK SKVSRRQPEE DYHTPSTVEI KTISHVIEEK GILLKLSVT DTPGFGDQVD NTNCWQPIMR HVNEQYEKYL NEEISIKRRK RIPDTRVHCC IYFIPPSGHS LRLVDIEVMK R LVEIVNVI PVIAKSDSLT LEERERFKAT IQQQLIEHNI RVYPDLENLD VDDETERQRN LKLKERLPFA IVGSSTTHQV GS KAVLGRK AGWGVIEVEN DAHCEFNHLR NMIIRTNLQD LKEVTAQVHY ELYRHRRLET LKKVPLDSVG STPSSPSYDI TNS EPNHKK VANTPKLGET GKAIAASQKE VVEALSESKI WSHPQFEK

UniProtKB: Neuronal-specific septin-3

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 529597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9bhw:
Septin Tetrameric Complex SEPT7/SEPT9 of Ciona intestinalis by Cryo-EM

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