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- EMDB-44552: Septin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44552
TitleSeptin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis by Cryo-EM
Map data
Sample
  • Complex: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
    • Protein or peptide: CiSeptin-2
    • Protein or peptide: CiSeptin-6
    • Protein or peptide: CiSeptin-7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsComplex / SPA / Cytoskeleton / Septin / CELL CYCLE
Function / homology
Function and homology information


septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / cilium assembly / kinetochore / cilium / microtubule cytoskeleton / molecular adaptor activity ...septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / cleavage furrow / cilium assembly / kinetochore / cilium / microtubule cytoskeleton / molecular adaptor activity / GTPase activity / GTP binding / cytosol
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
Biological speciesCiona intestinalis (vase tunicate)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMendonca DC / Pereira HM / Garratt RC
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/10247-0 Brazil
Sao Paulo Research Foundation (FAPESP)2023/06866-1 Brazil
Sao Paulo Research Foundation (FAPESP)2020/02897-1 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: Mendonca DC / Morais ST / Ciol H / Pinto AP / Leonardo DA / Valadares NF / Portugal RV / Klaholz BP / Garratt RC / Araujo AP
History
DepositionApr 22, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_44552.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.862 Å
Density
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-0.7119012 - 2.5311239
Average (Standard dev.)-0.0023685794 (±0.044186153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 441.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7

EntireName: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
Components
  • Complex: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
    • Protein or peptide: CiSeptin-2
    • Protein or peptide: CiSeptin-6
    • Protein or peptide: CiSeptin-7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7

SupramoleculeName: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Ciona intestinalis (vase tunicate)

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Macromolecule #1: CiSeptin-2

MacromoleculeName: CiSeptin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ciona intestinalis (vase tunicate)
Molecular weightTheoretical: 50.766543 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: CiSeptin-6

MacromoleculeName: CiSeptin-6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ciona intestinalis (vase tunicate)
Molecular weightTheoretical: 49.661637 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #3: CiSeptin-7

MacromoleculeName: CiSeptin-7 / type: protein_or_peptide / ID: 3 / 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 #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304274
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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