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- PDB-9cz2: Cryo-EM structure of a nautilus-like HflK/C assembly in complex w... -

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Basic information

Entry
Database: PDB / ID: 9cz2
TitleCryo-EM structure of a nautilus-like HflK/C assembly in complex with FtsH AAA protease
Components
  • ATP-dependent zinc metalloprotease FtsH
  • Modulator of FtsH protease HflC
  • Modulator of FtsH protease HflK
KeywordsCHAPERONE / FtsH / HflK / HflC / AAA protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / peptidase activity / hydrolase activity / cell division / ATP hydrolysis activity / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / peptidase activity / hydrolase activity / cell division / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
HflC / HflK / Menbrane protein HflK, N-terminal / Bacterial membrane protein N terminal / : / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Peptidase M41, FtsH extracellular ...HflC / HflK / Menbrane protein HflK, N-terminal / Bacterial membrane protein N terminal / : / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Band 7/SPFH domain superfamily / 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
Modulator of FtsH protease HflC / Protein HflK / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsGhanbarpour, A. / Sauer, R.T. / Davis, J.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: EMBO J / Year: 2025
Title: An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins.
Authors: Alireza Ghanbarpour / Bertina Telusma / Barrett M Powell / Jia Jia Zhang / Isabella Bolstad / Carolyn Vargas / Sandro Keller / Tania A Baker / Robert T Sauer / Joseph H Davis /
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 ...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.
History
DepositionAug 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
XA: Modulator of FtsH protease HflK
XB: Modulator of FtsH protease HflC
XC: Modulator of FtsH protease HflK
XD: Modulator of FtsH protease HflC
XE: Modulator of FtsH protease HflK
XF: Modulator of FtsH protease HflC
XG: Modulator of FtsH protease HflK
XH: Modulator of FtsH protease HflC
XI: Modulator of FtsH protease HflK
XJ: Modulator of FtsH protease HflC
XK: Modulator of FtsH protease HflK
XL: Modulator of FtsH protease HflC
XM: Modulator of FtsH protease HflK
XN: Modulator of FtsH protease HflC
XO: Modulator of FtsH protease HflK
XP: Modulator of FtsH protease HflC
XQ: Modulator of FtsH protease HflK
XR: Modulator of FtsH protease HflC
XS: Modulator of FtsH protease HflK
XT: Modulator of FtsH protease HflC
XU: Modulator of FtsH protease HflK
XX: Modulator of FtsH protease HflC
XV: Modulator of FtsH protease HflC
XW: Modulator of FtsH protease HflK
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH
D: ATP-dependent zinc metalloprotease FtsH
E: ATP-dependent zinc metalloprotease FtsH
F: ATP-dependent zinc metalloprotease FtsH
G: ATP-dependent zinc metalloprotease FtsH
H: ATP-dependent zinc metalloprotease FtsH
I: ATP-dependent zinc metalloprotease FtsH
J: ATP-dependent zinc metalloprotease FtsH
K: ATP-dependent zinc metalloprotease FtsH
L: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)1,849,19736
Polymers1,849,19736
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Modulator of FtsH protease HflK


Mass: 45598.793 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria)
Gene: hflK, hflK_1, A8502_001504, ACN81_01545, ACU57_19135, B6R15_002000, B6R31_000826, BANRA_02863, BGM66_001066, BGZ_01593, BGZ_05131, BJI68_16630, BK292_24855, BK383_13095, BTB68_003943, BTQ06_ ...Gene: hflK, hflK_1, A8502_001504, ACN81_01545, ACU57_19135, B6R15_002000, B6R31_000826, BANRA_02863, BGM66_001066, BGZ_01593, BGZ_05131, BJI68_16630, BK292_24855, BK383_13095, BTB68_003943, BTQ06_07290, BvCmsKKP061_03355, BXT93_16385, C0P57_000236, C3F40_14180, CF22_001630, CG704_01810, CIG67_23195, CQ842_09310, CQ842_12110, CTR35_001542, CV83915_01855, D4M65_22455, D9D43_14560, DD762_20800, DIV22_15560, DNQ45_06710, DS732_02655, DTL43_02345, DU321_10415, E2865_05442, E4K51_09085, E5H86_08375, E6D34_03745, EAI46_08375, ECs5150, EIZ93_17475, EN85_000830, EPS97_10200, F7N46_18140, F9461_18000, F9B07_05995, FGAF848_41630, FJQ40_01630, FKO60_18290, FOI11_014740, FOI11_20940, FPS11_03870, FVB16_06380, FWK02_13090, G3V95_10915, G4A38_03090, G4A47_10900, GAI89_04385, GAJ12_10750, GNW61_00325, GOP25_14130, GP965_11000, GP979_12080, GQA06_06275, GQE86_14305, GQM04_15800, GQM21_05505, GQW07_15995, GRO95_15840, GRW05_08865, GRW24_08520, GUC01_09055, H0O53_13460, H0O72_04915, HEP30_009475, HEP34_001782, HHH44_002336, HJQ60_002514, HLZ50_23395, HMV95_06705, HV109_21490, HV209_19960, HVW43_13980, I6H00_16150, I6H02_16705, J0541_002323, J5U05_001376, JNP96_03045, NCTC10082_01824, NCTC10429_04710, NCTC10974_05098, NCTC11181_01756, NCTC11341_03057, NCTC7922_05246, NCTC8500_05052, NCTC8959_04284, NCTC8960_02016, NCTC9044_02658, NCTC9045_05319, NCTC9077_05652, NCTC9117_05600, NCTC9702_05278, NCTC9706_01788, P6223_000677, QDW62_23495, RZR61_04275, SAMEA3472112_03401, SAMEA3752557_01673, WR15_07020
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C3SG32
#2: Protein
Modulator of FtsH protease HflC


Mass: 37703.887 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Gene: hflC, NCTC10418_06673 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A376L393
#3: Protein
ATP-dependent zinc metalloprotease FtsH


Mass: 70797.031 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria)
Gene: ftsH, hflB, A5U30_001984, ACN81_18510, ACU57_14510, AW118_08925, AWP47_10690, B6R15_000944, B6R31_001760, BCB93_002192, BE932_14805, BER14_09070, BG944_002117, BGM66_001548, BJI68_19380, BK292_ ...Gene: ftsH, hflB, A5U30_001984, ACN81_18510, ACU57_14510, AW118_08925, AWP47_10690, B6R15_000944, B6R31_001760, BCB93_002192, BE932_14805, BER14_09070, BG944_002117, BGM66_001548, BJI68_19380, BK292_10285, BK383_15900, BKL28_000230, BR158_000144, BTB68_000484, BTQ06_11805, BXT93_15525, C0P57_001801, C1Q91_000870, C2121_002705, C2M16_04280, C2R31_003415, C3F40_20440, C9Z68_06310, CF22_002939, CG704_16710, CIG67_17070, CQ842_08215, CQ842_15040, CTR35_000693, D3G36_08735, D4M65_02100, D4N09_15345, D9D43_03550, D9E49_09530, D9J61_00850, DD762_19175, DIV22_03040, DNX30_11300, DS732_23630, DTL43_04230, DU321_08605, E4K51_05415, E5H86_10330, E6D34_05680, EAI46_04455, ECs4057, EIA08_12565, EIZ93_11725, EN85_002286, EPS97_11790, EWK56_02840, F7F11_09100, F7N46_13565, F9413_10195, F9461_07370, F9B07_01200, FIJ20_03625, FJQ40_06950, FKO60_06175, FOI11_019860, FOI11_03320, FPI65_19695, FVB16_05835, FZU14_16135, G3V95_08710, G3W53_05000, G4A38_08240, G4A47_07630, G5603_15980, GAI89_03410, GAJ12_14295, GKF66_06520, GNW61_09600, GNZ05_17210, GOP25_03315, GP711_11120, GP954_10205, GP965_13355, GP975_09695, GQA06_10465, GQE86_15360, GQM04_01440, GQM13_09355, GQM21_01400, GQN34_18290, GQW07_03885, GRC73_09100, GRO95_03635, GRW05_19600, GRW24_08835, GUC01_10120, H0O72_09565, HEP30_003235, HEP34_000207, HHH44_002776, HI055_000339, HIE29_003230, HJQ60_002085, HLX92_02220, HLZ50_05410, HMV95_13920, HMW38_00475, HV109_02770, HVV39_08660, HVW04_18155, HVW43_19250, HVY77_03070, I6H00_21520, I6H02_11405, J0541_003213, J5U05_001194, JNP96_24695, OGM49_21720, P6223_000745, QDW62_02800, WR15_24505
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: C3SSK2, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FtsH.HflK.HflKC complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 50 nm
Image recordingElectron dose: 46.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionDetails: Patch CTF estimation, cryoSPARC / Type: NONE
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184019 / Symmetry type: POINT

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