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Yorodumi- EMDB-32003: Structural insights into the membrane microdomain organization by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32003 | |||||||||
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Title | Structural insights into the membrane microdomain organization by SPFH family proteins | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane microdomain organization / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information regulation of peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / peptidase activity / membrane => GO:0016020 / cell division / zinc ion binding / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Ma CY / Wang CK | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32003.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-32003-v30.xml emd-32003.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_32003.png | 138.4 KB | ||
Filedesc metadata | emd-32003.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32003 | HTTPS FTP |
-Validation report
Summary document | emd_32003_validation.pdf.gz | 348.4 KB | Display | EMDB validaton report |
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Full document | emd_32003_full_validation.pdf.gz | 348 KB | Display | |
Data in XML | emd_32003_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_32003_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32003 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32003 | HTTPS FTP |
-Related structure data
Related structure data | 7vhqMC 7vhpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32003.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : KCF complex
Entire | Name: KCF complex |
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Components |
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-Supramolecule #1: KCF complex
Supramolecule | Name: KCF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: ATP-dependent zinc metalloprotease FtsH
Macromolecule | Name: 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 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 7.345267 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RKVDYSTFLQ EVNNDQVREA RINGREINVT KKDSNRYTTY IPVQDPKLLD NLLTKNVKVV GEP UniProtKB: ATP-dependent zinc metalloprotease FtsH |
-Macromolecule #2: Protein HflK
Macromolecule | Name: Protein HflK / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 30.164129 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RVVTIAAAAI VIIWAASGFY TIKEAERGVV TRFGKFSHLV EPGLNWKPTF IDEVKPVNVE AVRELAASGV MLTSDENVVR VEMNVQYRV TNPEKYLYSV TSPDDSLRQA TDSALRGVIG KYTMDRILTE GRTVIRSDTQ RELEETIRPY DMGITLLDVN F QAARPPEE ...String: RVVTIAAAAI VIIWAASGFY TIKEAERGVV TRFGKFSHLV EPGLNWKPTF IDEVKPVNVE AVRELAASGV MLTSDENVVR VEMNVQYRV TNPEKYLYSV TSPDDSLRQA TDSALRGVIG KYTMDRILTE GRTVIRSDTQ RELEETIRPY DMGITLLDVN F QAARPPEE VKAAFDDAIA ARENEQQYIR EAEAYTNEVQ PRANGQAQRI LEEARAYKAQ TILEAQGEVA RFAKLLPEYK AA PEITRER LYIETMEKVL GNTRKVLVND UniProtKB: Protein HflK |
-Macromolecule #3: Modulator of FtsH protease HflC
Macromolecule | Name: Modulator of FtsH protease HflC / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 37.176293 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRKSVIAIII IVLVVLYMSV FVVKEGERGI TLRFGKVLRD DDNKPLVYEP GLHFKIPFIE TVKMLDARIQ TMDNQADRFV TKEKKDLIV DSYIKWRISD FSRYYLATGG GDISQAEVLL KRKFSDRLRS EIGRLDVKDI VTDSRGRLTL EVRDALNSGS A GTEDEVTT ...String: MRKSVIAIII IVLVVLYMSV FVVKEGERGI TLRFGKVLRD DDNKPLVYEP GLHFKIPFIE TVKMLDARIQ TMDNQADRFV TKEKKDLIV DSYIKWRISD FSRYYLATGG GDISQAEVLL KRKFSDRLRS EIGRLDVKDI VTDSRGRLTL EVRDALNSGS A GTEDEVTT SAADNAIAEA AERVTAETKG KVPVINPNSM AALGIEVVDV RIKQINLPTE VSEAIYNRMR AEREAVARRH RS QGQEEAE KLRATADYEV TRTLAEAERQ GRIMRGEGDA EAAKLFADAF SKDPDFYAFI RSLRAYENSF SGNQDVMVMS PDS DFFRYM KTP UniProtKB: Modulator of FtsH protease HflC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274457 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |