[English] 日本語
Yorodumi
- PDB-9bht: Septin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bht
TitleSeptin Hexameric Complex SEPT2/SEPT6/SEPT7 of Ciona intestinalis by Cryo-EM
Components
  • CiSeptin-2
  • CiSeptin-6
  • CiSeptin-7
KeywordsCELL CYCLE / Complex / SPA / Cytoskeleton / Septin
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Septin / Septin
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMendonca, D.C. / Pereira, H.M. / Garratt, R.C.
Funding support Brazil, 3items
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, D.C. / Morais, S.T. / Ciol, H. / Pinto, A.P. / Leonardo, D.A. / D’Muniz Pereira, H. / Valadares, N.F. / Portugal, R.V. / Klaholz, B.P. / Garratt, R.C. / Araujo, A.P.
History
DepositionApr 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CiSeptin-2
B: CiSeptin-6
C: CiSeptin-7
D: CiSeptin-7
E: CiSeptin-6
F: CiSeptin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,21412
Polymers298,3946
Non-polymers2,8196
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein CiSeptin-2


Mass: 50766.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein CiSeptin-6


Mass: 49661.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6V5P8
#3: Protein CiSeptin-7


Mass: 48769.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2Y169
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ciona intestinalis Septin Hexameric Complex SEPT2/SEPT6/SEPT7
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Ciona intestinalis (vase tunicate)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304274 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412960
ELECTRON MICROSCOPYf_angle_d0.94717528
ELECTRON MICROSCOPYf_dihedral_angle_d12.1421740
ELECTRON MICROSCOPYf_chiral_restr0.0491972
ELECTRON MICROSCOPYf_plane_restr0.0052219

+
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