[English] 日本語
Yorodumi
- EMDB-44555: Septin Tetrameric Complex SEPT7/SEPT9 of Ciona intestinalis by Cryo-EM -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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: 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

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_44555.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map
Voxel sizeX=Y=Z: 0.729 Å
Density
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 °

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more