[English] 日本語
Yorodumi
- EMDB-64825: Structure of FtsZ1 in complex with GMPCPP from Candidatus Odinarc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64825
TitleStructure of FtsZ1 in complex with GMPCPP from Candidatus Odinarchaeota
Map dataThis is the final sharpened map with helical symmetry imposed. The contour level is based on values shown in chimera
Sample
  • Complex: FtsZ1 protein in complex with GMPCPP
    • Protein or peptide: Cell division protein FtsZ
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
KeywordsCell division Protein / CELL CYCLE
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain ...Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Cell division protein FtsZ
Similarity search - Component
Biological speciesCandidatus Odinarchaeota (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBose S / Kutti RV
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: EMBO J / Year: 2025
Title: Distinct filament morphology and membrane tethering features of the dual FtsZ paralogs in Odinarchaeota.
Authors: Jayanti Kumari / Akhilesh Uthaman / Sucharita Bose / Ananya Kundu / Vaibhav Sharma / Soumyajit Dutta / Anubhav Dhar / Srijita Roy / Ramanujam Srinivasan / Samay Pande / Kutti R Vinothkumar / ...Authors: Jayanti Kumari / Akhilesh Uthaman / Sucharita Bose / Ananya Kundu / Vaibhav Sharma / Soumyajit Dutta / Anubhav Dhar / Srijita Roy / Ramanujam Srinivasan / Samay Pande / Kutti R Vinothkumar / Pananghat Gayathri / Saravanan Palani /
Abstract: The Asgard phylum has emerged as a model to study eukaryogenesis because of their close relatedness with the eukaryotes. In this study, we use FtsZ proteins from a member of the class Odinarchaeia as ...The Asgard phylum has emerged as a model to study eukaryogenesis because of their close relatedness with the eukaryotes. In this study, we use FtsZ proteins from a member of the class Odinarchaeia as representatives to investigate the probable origin, evolution, and assembly of the FtsZ/tubulin protein superfamily in Asgard archaea. We performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the anchor OdinSepF via OdinFtsZ2's C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting. Our findings highlight the diversity of FtsZ proteins in the archaeal phylum Asgardarchaeota, providing valuable insights into the evolution and differentiation of tubulin-family proteins.
History
DepositionMay 28, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64825.png

Downloads & links

-
Map

FileDownload / File: emd_64825.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the final sharpened map with helical symmetry imposed. The contour level is based on values shown in chimera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.5401502 - 2.7509565
Average (Standard dev.)0.004211511 (±0.0689053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: This is half map A. This is unsharpened map....

Fileemd_64825_half_map_1.map
AnnotationThis is half map_A. This is unsharpened map. The contour level is based on values shown in chimera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: This is half map B. This is unsharpened map....

Fileemd_64825_half_map_2.map
AnnotationThis is half map_B. This is unsharpened map. The contour level is based on values shown in chimera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FtsZ1 protein in complex with GMPCPP

EntireName: FtsZ1 protein in complex with GMPCPP
Components
  • Complex: FtsZ1 protein in complex with GMPCPP
    • Protein or peptide: Cell division protein FtsZ
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

-
Supramolecule #1: FtsZ1 protein in complex with GMPCPP

SupramoleculeName: FtsZ1 protein in complex with GMPCPP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candidatus Odinarchaeota (archaea)
Molecular weightTheoretical: 8.8 kDa/nm

-
Macromolecule #1: Cell division protein FtsZ

MacromoleculeName: Cell division protein FtsZ / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Odinarchaeota (archaea)
Molecular weightTheoretical: 38.742777 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIYMRTLIKS ALSKARVEDY TKEDSEIEDT LRDAKAKITV IGVGGAGNNT ITRLKMEGVE GATTVAVNTD AQGLLHTISD QKILLGKQL TKGLGAGNDP KIGEAAAKEA IEELREVVKS DMIFITCGLG GGTGTGAAPV IAELAKEEKA LTVSIVTLPF K AEGVKREA ...String:
MIYMRTLIKS ALSKARVEDY TKEDSEIEDT LRDAKAKITV IGVGGAGNNT ITRLKMEGVE GATTVAVNTD AQGLLHTISD QKILLGKQL TKGLGAGNDP KIGEAAAKEA IEELREVVKS DMIFITCGLG GGTGTGAAPV IAELAKEEKA LTVSIVTLPF K AEGVKREA NARWGLEQLL KVCDSVIVIP NDRILEIAPE LSLNEAFRLA DEILIGGVKG ITELIFKPGL INLDFADVKK VM NNKGTAI IGMAESASNN SAVEAVELAI SNPLLDVDVS KASAALINLC GGPNLTIKHA EEAIRCVAKK IREDAEIIWG VII DQDMGK LTRATVILSG LQPRQLDENQ IDKKVINKSA KLALDEL

UniProtKB: Cell division protein FtsZ

-
Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 3110 / Average exposure time: 60.0 sec. / Average electron dose: 23.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 356932
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9v7v:
Structure of FtsZ1 in complex with GMPCPP from Candidatus Odinarchaeota

+
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://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