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Basic information

Entry
Database: PDB / ID: 7vhq
TitleStructural insights into the membrane microdomain organization by SPFH family proteins
Components
  • ATP-dependent zinc metalloprotease FtsH
  • Modulator of FtsH protease HflC
  • Protein HflK
KeywordsMEMBRANE PROTEIN / membrane microdomain organization
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / membrane => GO:0016020 / protein catabolic process / metalloendopeptidase activity / peptidase activity / cell division / proteolysis / zinc ion binding / ATP binding ...Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / membrane => GO:0016020 / protein catabolic process / metalloendopeptidase activity / peptidase activity / cell division / 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 / 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 / Band 7/SPFH domain superfamily / 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
Protein HflK / ATP-dependent zinc metalloprotease FtsH / Modulator of FtsH protease HflC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsMa, C.Y. / Wang, C.K. / Luo, D.Y. / Yan, L. / Yang, W.X. / Li, N.N. / Gao, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2022
Title: Structural insights into the membrane microdomain organization by SPFH family proteins.
Authors: Chengying Ma / Chengkun Wang / Dingyi Luo / Lu Yan / Wenxian Yang / Ningning Li / Ning Gao /
Abstract: The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and ...The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and eukaryotes. The widespread Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are enriched in functional membrane microdomains at various subcellular locations, and therefore were hypothesized to play a scaffolding role in microdomain formation. In addition, many SPFH proteins are also implicated in highly specific processes occurring on the membrane. However, none of these functions is understood at the molecular level. Here we report the structure of a supramolecular complex that is isolated from bacterial membrane microdomains and contains two SPFH proteins (HflK and HflC) and a membrane-anchored AAA+ protease FtsH. HflK and HflC form a circular 24-mer assembly, featuring a laterally segregated membrane microdomain (20 nm in diameter) bordered by transmembrane domains of HflK/C and a completely sealed periplasmic vault. Four FtsH hexamers are embedded inside this microdomain through interactions with the inner surface of the vault. These observations provide a mechanistic explanation for the role of HflK/C and their mitochondrial homologs prohibitins in regulating membrane-bound AAA+ proteases, and suggest a general model for the organization and functionalization of membrane microdomains by SPFH proteins.
History
DepositionSep 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
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: Protein HflK
F: Protein HflK
G: Modulator of FtsH protease HflC
H: Modulator of FtsH protease HflC
I: Modulator of FtsH protease HflC
U: Protein HflK
e: ATP-dependent zinc metalloprotease FtsH
f: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)246,09312
Polymers246,09312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area48760 Å2
ΔGint-299 kcal/mol
Surface area104400 Å2

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Components

#1: Protein
ATP-dependent zinc metalloprotease FtsH


Mass: 7345.267 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsH, BvCms35BK_01530, NCTC13127_00921 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A376T6B9, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein Protein HflK


Mass: 30164.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GJ11_26185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A193M0W2
#3: Protein Modulator of FtsH protease HflC


Mass: 37176.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hflC, D4U49_22000, D7Y10_19420 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R1A7Q4

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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: KCF complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274457 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316890
ELECTRON MICROSCOPYf_angle_d0.55122803
ELECTRON MICROSCOPYf_dihedral_angle_d4.122331
ELECTRON MICROSCOPYf_chiral_restr0.0432589
ELECTRON MICROSCOPYf_plane_restr0.0042985

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