9CZ2 | pdb_00009cz2

Cryo-EM structure of a nautilus-like HflK/C assembly in complex with FtsH AAA protease

  • Classification: CHAPERONE
  • Organism(s): Escherichia coli BL21
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2024-08-03 Released: 2024-11-13 
  • Deposition Author(s): Ghanbarpour, A., Sauer, R.T., Davis, J.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins.

Ghanbarpour, A.Telusma, B.Powell, B.M.Zhang, J.J.Bolstad, I.Vargas, C.Keller, S.Baker, T.A.Sauer, R.T.Davis, J.H.

(2025) EMBO J 44: 2501-2513

  • DOI: https://doi.org/10.1038/s44318-025-00408-1
  • Primary Citation of Related Structures:  
    9CZ2

  • PubMed Abstract: 

    The AAA protease FtsH associates with HflK/C subunits to form a megadalton-size complex that spans the inner membrane and extends into the periplasm of E. coli. How this bacterial complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following the overproduction of protein components, recent cryo-EM structures showed symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit the degradation of membrane-embedded substrates. Here, we present structures of native protein complexes, in which HflK/C instead forms an asymmetric nautilus-shaped assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. Membrane curvature in our FtsH•HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.


  • Organizational Affiliation
    • Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02129, USA. alirezag@wustl.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Modulator of FtsH protease HflK419Escherichia coli BL21Mutation(s): 0 
Gene Names: 
hflKhflK_1A8502_001504ACN81_01545ACU57_19135B6R15_002000B6R31_000826BANRA_02863BGM66_001066BGZ_01593BGZ_05131BJI68_16630BK292_24855BK383_13095BTB68_003943BTQ06_07290BvCmsKKP061_03355BXT93_16385C0P57_000236C3F40_14180CF22_001630CG704_01810CIG67_23195CQ842_09310CQ842_12110CTR35_001542CV83915_01855D4M65_22455D9D43_14560DD762_20800DIV22_15560DNQ45_06710DS732_02655DTL43_02345DU321_10415E2865_05442E4K51_09085E5H86_08375E6D34_03745EAI46_08375ECs5150EIZ93_17475EN85_000830EPS97_10200F7N46_18140F9461_18000F9B07_05995FGAF848_41630FJQ40_01630FKO60_18290FOI11_014740FOI11_20940FPS11_03870FVB16_06380FWK02_13090G3V95_10915G4A38_03090G4A47_10900GAI89_04385GAJ12_10750GNW61_00325GOP25_14130GP965_11000GP979_12080GQA06_06275GQE86_14305GQM04_15800GQM21_05505GQW07_15995GRO95_15840GRW05_08865GRW24_08520GUC01_09055H0O53_13460H0O72_04915HEP30_009475HEP34_001782HHH44_002336HJQ60_002514HLZ50_23395HMV95_06705HV109_21490HV209_19960HVW43_13980I6H00_16150I6H02_16705J0541_002323J5U05_001376JNP96_03045NCTC10082_01824NCTC10429_04710NCTC10974_05098NCTC11181_01756NCTC11341_03057NCTC7922_05246NCTC8500_05052NCTC8959_04284NCTC8960_02016NCTC9044_02658NCTC9045_05319NCTC9077_05652NCTC9117_05600NCTC9702_05278NCTC9706_01788P6223_000677QDW62_23495RZR61_04275SAMEA3472112_03401SAMEA3752557_01673WR15_07020

UniProt
Find proteins for P0ABC7 (Escherichia coli (strain K12))
Explore P0ABC7 
Go to UniProtKB:  P0ABC7
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UniProt GroupP0ABC7
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Modulator of FtsH protease HflC334Escherichia coli BL21Mutation(s): 0 
Gene Names: hflCNCTC10418_06673
UniProt
Find proteins for P0ABC3 (Escherichia coli (strain K12))
Explore P0ABC3 
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UniProt GroupP0ABC3
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent zinc metalloprotease FtsH644Escherichia coli BL21Mutation(s): 0 
Gene Names: 
ftsHhflBA5U30_001984ACN81_18510ACU57_14510AW118_08925AWP47_10690B6R15_000944B6R31_001760BCB93_002192BE932_14805BER14_09070BG944_002117BGM66_001548BJI68_19380BK292_10285BK383_15900BKL28_000230BR158_000144BTB68_000484BTQ06_11805BXT93_15525C0P57_001801C1Q91_000870C2121_002705C2M16_04280C2R31_003415C3F40_20440C9Z68_06310CF22_002939CG704_16710CIG67_17070CQ842_08215CQ842_15040CTR35_000693D3G36_08735D4M65_02100D4N09_15345D9D43_03550D9E49_09530D9J61_00850DD762_19175DIV22_03040DNX30_11300DS732_23630DTL43_04230DU321_08605E4K51_05415E5H86_10330E6D34_05680EAI46_04455ECs4057EIA08_12565EIZ93_11725EN85_002286EPS97_11790EWK56_02840F7F11_09100F7N46_13565F9413_10195F9461_07370F9B07_01200FIJ20_03625FJQ40_06950FKO60_06175FOI11_019860FOI11_03320FPI65_19695FVB16_05835FZU14_16135G3V95_08710G3W53_05000G4A38_08240G4A47_07630G5603_15980GAI89_03410GAJ12_14295GKF66_06520GNW61_09600GNZ05_17210GOP25_03315GP711_11120GP954_10205GP965_13355GP975_09695GQA06_10465GQE86_15360GQM04_01440GQM13_09355GQM21_01400GQN34_18290GQW07_03885GRC73_09100GRO95_03635GRW05_19600GRW24_08835GUC01_10120H0O72_09565HEP30_003235HEP34_000207HHH44_002776HI055_000339HIE29_003230HJQ60_002085HLX92_02220HLZ50_05410HMV95_13920HMW38_00475HV109_02770HVV39_08660HVW04_18155HVW43_19250HVY77_03070I6H00_21520I6H02_11405J0541_003213J5U05_001194JNP96_24695OGM49_21720P6223_000745QDW62_02800WR15_24505

EC: 3.4.24
UniProt
Find proteins for P0AAI3 (Escherichia coli (strain K12))
Explore P0AAI3 
Go to UniProtKB:  P0AAI3
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAI3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14_3260:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01-GM144542
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM141517
National Science Foundation (NSF, United States)United States2046778

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references