[English] 日本語
Yorodumi
- EMDB-43580: CryoEM Structure of a FtsH Helical Assembly in the Aged State -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43580
TitleCryoEM Structure of a FtsH Helical Assembly in the Aged State
Map data
Sample
  • Complex: CryoEM Structure of a FtsH Helical Assembly in the Aged State
    • Protein or peptide: ATP-dependent zinc metalloprotease FtsH
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsnucleotide binding / protease / cytoplasmic domain / helical assembly / HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi Y / Zhu J / Zhang Z / Wang F / Egelman EH / Tezcan FA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2004558 United States
Department of Energy (DOE, United States)DE-SC0003844 United States
Department of Energy (DOE, United States)DE-SC0019288 United States
CitationJournal: Nat Chem Biol / Year: 2025
Title: Transforming an ATP-dependent enzyme into a dissipative, self-assembling system.
Authors: Yiying Li / Jie Zhu / Zhiyin Zhang / Jiapeng Wei / Fengbin Wang / Georg Meisl / Tuomas P J Knowles / Edward H Egelman / F Akif Tezcan /
Abstract: Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials ...Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5'-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Here we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution.
History
DepositionJan 31, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43580.png

Downloads & links

-
Map

FileDownload / File: emd_43580.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 385.28 Å		0.86 Å/pix.
x 448 pix.
= 385.28 Å		0.86 Å/pix.
x 448 pix.
= 385.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.6622089 - 4.622275
Average (Standard dev.)0.015922088 (±0.13643661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 385.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43580_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43580_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CryoEM Structure of a FtsH Helical Assembly in the Aged State

EntireName: CryoEM Structure of a FtsH Helical Assembly in the Aged State
Components
  • Complex: CryoEM Structure of a FtsH Helical Assembly in the Aged State
    • Protein or peptide: ATP-dependent zinc metalloprotease FtsH
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: CryoEM Structure of a FtsH Helical Assembly in the Aged State

SupramoleculeName: CryoEM Structure of a FtsH Helical Assembly in the Aged State
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermotoga maritima (bacteria)

-
Macromolecule #1: ATP-dependent zinc metalloprotease FtsH

MacromoleculeName: ATP-dependent zinc metalloprotease FtsH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 51.493832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGGATMYKPS GNKRVTFKDV GGAEEAIEEL KEVVEFLKDP SKFNRIGARM PKGILLVGPP GTGKTLLARA VAGEANVPFF HISGSDFVE LFVGVGAARV RDLFAQAKAH APSIVFIDEI DAVGRHRGAG LGGGHDEREQ TLNQLLVEMD GFDSKEGIIV M AATNRPDI ...String:
SGGATMYKPS GNKRVTFKDV GGAEEAIEEL KEVVEFLKDP SKFNRIGARM PKGILLVGPP GTGKTLLARA VAGEANVPFF HISGSDFVE LFVGVGAARV RDLFAQAKAH APSIVFIDEI DAVGRHRGAG LGGGHDEREQ TLNQLLVEMD GFDSKEGIIV M AATNRPDI LDPALLRPGR FDKKIVVDPP DMLGRKKILE IHTRNKPLAE DVNLEIIAKR TPGFVGADLE NLVNEAALLA AR EGRDKIT MKDFEEAIDR VIAGPARKSL LISPAEKRII AYHEAGHAVV STVVPNGEPV HRISIIPRGY KALGYTLHLP EED KYLVSR NELLDKLTAL LGGRAAEEVV FGDVTSGAAN DIERATEIAR NMVSQLGMSE ELGPLAWGKE EQEVFLGKEI TRLR NYSEE VASKIDEEVK KIVTNSYERA KEIIRKYRKQ LDNIVEILLE KETIEGDELR RILSEEFEKV VE

UniProtKB: ATP-dependent zinc metalloprotease FtsH

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
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: 9.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 157.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2781039
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3kds

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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