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- EMDB-25837: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state -

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Basic information

Entry
Database: EMDB / ID: EMD-25837
TitleCryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state
Map data
Sample
  • Complex: Hexameric FtsH in the ADP-bound state
    • Protein or peptide: ATP-dependent zinc metalloprotease FtsH
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ ATPase / protease / hexamer / ADP-bound state / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLiu W / Schoonen M
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Commun Biol / Year: 2022
Title: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state.
Authors: Wu Liu / Martien Schoonen / Tong Wang / Sean McSweeney / Qun Liu /
Abstract: AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of ...AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.
History
DepositionJan 2, 2022-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25837.png

Downloads & links

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Map

FileDownload / File: emd_25837.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 200 pix.
= 273.68 Å		1.37 Å/pix.
x 200 pix.
= 273.68 Å		1.37 Å/pix.
x 200 pix.
= 273.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3684 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-1.0967261 - 2.8982875
Average (Standard dev.)0.011758418 (±0.110866986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 273.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Hexameric FtsH in the ADP-bound state

EntireName: Hexameric FtsH in the ADP-bound state
Components
  • Complex: Hexameric FtsH in the ADP-bound state
    • Protein or peptide: ATP-dependent zinc metalloprotease FtsH
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Hexameric FtsH in the ADP-bound state

SupramoleculeName: Hexameric FtsH in the ADP-bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermotoga maritima (bacteria)

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Macromolecule #1: ATP-dependent zinc metalloprotease FtsH

MacromoleculeName: ATP-dependent zinc metalloprotease FtsH / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 68.489664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMNRSNIW NLLFTILIIV TLFWLARFFY VENSPVSKLS YTSFVQMVED ERSVVSEVVI RDDGVLRVYT KDGRVYEVDA PWAVNDSQL IEKLVSKGIK VSGERSGSSS FWINVLGTLI PTILFIVVWL FIMRSLSGRN NQAFTFTKSR ATMYKPSGNK R VTFKDVGG ...String:
SNAMNRSNIW NLLFTILIIV TLFWLARFFY VENSPVSKLS YTSFVQMVED ERSVVSEVVI RDDGVLRVYT KDGRVYEVDA PWAVNDSQL IEKLVSKGIK VSGERSGSSS FWINVLGTLI PTILFIVVWL FIMRSLSGRN NQAFTFTKSR ATMYKPSGNK R VTFKDVGG AEEAIEELKE VVEFLKDPSK FNRIGARMPK GILLVGPPGT GKTLLARAVA GEANVPFFHI SGSDFVELFV GV GAARVRD LFAQAKAHAP CIVFIDEIDA VGRHRGAGLG GGHDEREQTL NQLLVEMDGF DSKEGIIVMA ATNRPDILDP ALL RPGRFD KKIVVDPPDM LGRKKILEIH TRNKPLAEDV NLEIIAKRTP GFVGADLENL VNEAALLAAR EGRDKITMKD FEEA IDRVI AGPARKSKLI SPKEKRIIAY YEAGHAVVST VVPNGEPVHR ISIIPRGYKA LGYTLHLPEE DKYLVSRNEL LDKLT ALLG GRAAEEVVFG DVTSGAANDI ERATEIARNM VCQLGMSEEL GPLAWGKEEQ EVFLGKEITR LRNYSEEVAS KIDEEV KKI VTNCYERAKE IIRKYRKQLD NIVEILLEKE TIEGDELRRI LSEEFEKVVE

UniProtKB: ATP-dependent zinc metalloprotease FtsH

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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: 7.6
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 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: 0.7000000000000001 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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86652
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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