+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32520 | |||||||||
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Title | Cryo-EM structure of E.coli membrane protein complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information : / membrane protein complex / negative regulation of peptidase activity / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / response to heat / ATP hydrolysis activity ...: / membrane protein complex / negative regulation of peptidase activity / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / response to heat / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Qiao Z / Gao YG | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32520.map.gz | 75.1 MB | EMDB map data format | |
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Header (meta data) | emd-32520-v30.xml emd-32520.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_32520.png | 142.8 KB | ||
Filedesc metadata | emd-32520.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32520 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32520 | HTTPS FTP |
-Validation report
Summary document | emd_32520_validation.pdf.gz | 427.7 KB | Display | EMDB validaton report |
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Full document | emd_32520_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | emd_32520_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_32520_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32520 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32520 | HTTPS FTP |
-Related structure data
Related structure data | 7wi3MC 7wi4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32520.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3728 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : E.Coli protein complex
Entire | Name: E.Coli protein complex |
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Components |
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-Supramolecule #1: E.Coli protein complex
Supramolecule | Name: E.Coli protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-Macromolecule #1: Modulator of FtsH protease HflC
Macromolecule | Name: Modulator of FtsH protease HflC / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 37.703887 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 PAADNAIAEA AERVTAETKG KVPVINPNSM AALGIEVVDV RIKQINLPTE VSEAIYNRMR AEREAVARRH RS QGQEEAE KLRATADYEV TRTLAEAERQ GRIMRGEGDA EAAKLFADAF SKDPDFYAFI RSLRAYENSF SGNQDVMVMS PDS DFFRYM KTPTSATR UniProtKB: Modulator of FtsH protease HflC |
-Macromolecule #2: Modulator of FtsH protease HflK
Macromolecule | Name: Modulator of FtsH protease HflK / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 45.598793 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAWNQPGNNG QDRDPWGSSK PGGNSEGNGN KGGRDQGPPD LDDIFRKLSK KLGGLGGGKG TGSGGGSSSQ GPRPQLGGRV VTIAAAAIV IIWAASGFYT IKEAERGVVT RFGKFSHLVE PGLNWKPTFI DEVKPVNVEA VRELAASGVM LTSDENVVRV E MNVQYRVT ...String: MAWNQPGNNG QDRDPWGSSK PGGNSEGNGN KGGRDQGPPD LDDIFRKLSK KLGGLGGGKG TGSGGGSSSQ GPRPQLGGRV VTIAAAAIV IIWAASGFYT IKEAERGVVT RFGKFSHLVE PGLNWKPTFI DEVKPVNVEA VRELAASGVM LTSDENVVRV E MNVQYRVT NPEKYLYSVT SPDDSLRQAT DSALRGVIGK YTMDRILTEG RTVIRSDTQR ELEETIRPYD MGITLLDVNF QA ARPPEEV KAAFDDAIAA RENEQQYIRE AEAYTNEVQP RANGQAQRIL EEARAYKAQT ILEAQGEVAR FAKLLPEYKA APE ITRERL YIETMEKVLG NTRKVLVNDK GGNLMVLPLD QMLKGGNAPA AKSDNGASNL LRLPPASSST TSGASNTSST SQGD IMDQR RANAQRNDYQ RQGE UniProtKB: Modulator of FtsH protease HflK |
-Macromolecule #3: ATP-dependent zinc metalloprotease FtsH
Macromolecule | Name: ATP-dependent zinc metalloprotease FtsH / type: protein_or_peptide / ID: 3 / Number of copies: 24 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 70.797031 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAKNLILWLV IAVVLMSVFQ SFGPSESNGR KVDYSTFLQE VNNDQVREAR INGREINVTK KDSNRYTTYI PVQDPKLLDN LLTKNVKVV GEPPEEPSLL ASIFISWFPM LLLIGVWIFF MRQMQGGGGK GAMSFGKSKA RMLTEDQIKT TFADVAGCDE A KEEVAELV ...String: MAKNLILWLV IAVVLMSVFQ SFGPSESNGR KVDYSTFLQE VNNDQVREAR INGREINVTK KDSNRYTTYI PVQDPKLLDN LLTKNVKVV GEPPEEPSLL ASIFISWFPM LLLIGVWIFF MRQMQGGGGK GAMSFGKSKA RMLTEDQIKT TFADVAGCDE A KEEVAELV EYLREPSRFQ KLGGKIPKGV LMVGPPGTGK TLLAKAIAGE AKVPFFTISG SDFVEMFVGV GASRVRDMFE QA KKAAPCI IFIDEIDAVG RQRGAGLGGG HDEREQTLNQ MLVEMDGFEG NEGIIVIAAT NRPDVLDPAL LRPGRFDRQV VVG LPDVRG REQILKVHMR RVPLAPDIDA AIIARGTPGF SGADLANLVN EAALFAARGN KRVVSMVEFE KAKDKIMMGA ERRS MVMTE AQKESTAYHE AGHAIIGRLV PEHDPVHKVT IIPRGRALGV TFFLPEGDAI SASRQKLESQ ISTLYGGRLA EEIIY GPEH VSTGASNDIK VATNLARNMV TQWGFSEKLG PLLYAEEEGE VFLGRSVAKA KHMSDETARI IDQEVKALIE RNYNRA RQL LTDNMDILHA MKDALMKYET IDAPQIDDLM ARRDVRPPAG WEEPGASNNS GDNGSPKAPR PVDEPRTPNP GNTMSEQ LG DK UniProtKB: ATP-dependent zinc metalloprotease FtsH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26863 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |