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- EMDB-32524: Cryo-EM map of E.coli FtsH AAA protease -

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Basic information

Entry
Database: EMDB / ID: EMD-32524
TitleCryo-EM map of E.coli FtsH AAA protease
Map data
Sample
  • Complex: FtsH
    • Protein or peptide: E.Coli FtsH AAA protease
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsQiao Z / Gao YG
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Cell Rep / Year: 2022
Title: Cryo-EM structure of the entire FtsH-HflKC AAA protease complex.
Authors: Zhu Qiao / Tatsuhiko Yokoyama / Xin-Fu Yan / Ing Tsyr Beh / Jian Shi / Sandip Basak / Yoshinori Akiyama / Yong-Gui Gao /
Abstract: The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic ...The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC complex, comprising 12 copies of both HflK and HflC, all of which interact reciprocally to form a cage, as well as four FtsH hexamers with periplasmic domains and transmembrane helices enclosed inside the cage and cytoplasmic domains situated at the base of the cage. FtsH K61/D62/S63 in the β2-β3 loop in the periplasmic domain directly interact with HflK, contributing to complex formation. Pull-down and in vivo enzymatic activity assays validate the importance of the interacting interface for FtsH-HflKC complex formation. Structural comparison with the substrate-bound human m-AAA protease AFG3L2 offers implications for the HflKC cage in modulating substrate access to FtsH. Together, our findings provide a better understanding of FtsH-type AAA protease holoenzyme assembly and regulation.
History
DepositionJan 2, 2022-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJun 15, 2022-
Current statusJun 15, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32524.png

Downloads & links

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Map

FileDownload / File: emd_32524.map.gz / Format: CCP4 / Size: 15.6 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 160 pix.
= 219.648 Å		1.37 Å/pix.
x 160 pix.
= 219.648 Å		1.37 Å/pix.
x 160 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.006388682 - 0.041628283
Average (Standard dev.)0.0007368119 (±0.0037065658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 219.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : FtsH

EntireName: FtsH
Components
  • Complex: FtsH
    • Protein or peptide: E.Coli FtsH AAA protease

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Supramolecule #1: FtsH

SupramoleculeName: FtsH / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: E.Coli FtsH AAA protease

MacromoleculeName: E.Coli FtsH AAA protease / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKNLILWLV IAVVLMSVFQ SFGPSESNGR KVDYSTFLQE VNNDQVREAR INGREINVTK KDSNRYTTY IPVQDPKLLD NLLTKNVKVV GEPPEEPSLL ASIFISWFPM LLLIGVWIFF M RQMQGGGG KGAMSFGKSK ARMLTEDQIK TTFADVAGCD EAKEEVAELV ...String:
MAKNLILWLV IAVVLMSVFQ SFGPSESNGR KVDYSTFLQE VNNDQVREAR INGREINVTK KDSNRYTTY IPVQDPKLLD NLLTKNVKVV GEPPEEPSLL ASIFISWFPM LLLIGVWIFF M RQMQGGGG KGAMSFGKSK ARMLTEDQIK TTFADVAGCD EAKEEVAELV EYLREPSRFQ KL GGKIPKG VLMVGPPGTG KTLLAKAIAG EAKVPFFTIS GSDFVEMFVG VGASRVRDMF EQA KKAAPC IIFIDEIDAV GRQRGAGLGG GHDEREQTLN QMLVEMDGFE GNEGIIVIAA TNRP DVLDP ALLRPGRFDR QVVVGLPDVR GREQILKVHM RRVPLAPDID AAIIARGTPG FSGAD LANL VNEAALFAAR GNKRVVSMVE FEKAKDKIMM GAERRSMVMT EAQKESTAYH EAGHAI IGR LVPEHDPVHK VTIIPRGRAL GVTFFLPEGD AISASRQKLE SQISTLYGGR LAEEIIY GP EHVSTGASND IKVATNLARN MVTQWGFSEK LGPLLYAEEE GEVFLGRSVA KAKHMSDE T ARIIDQEVKA LIERNYNRAR QLLTDNMDIL HAMKDALMKY ETIDAPQIDD LMARRDVRP PAGWEEPGAS NNSGDNGSPK APRPVDEPRT PNPGNTMSEQ LGDK

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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

Concentration0.6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40539
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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