+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32521 | |||||||||
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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 / HYDROLASE | |||||||||
Function / homology | Function and homology information membrane protein complex / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_32521.map.gz | 13.9 MB | EMDB map data format | |
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Header (meta data) | emd-32521-v30.xml emd-32521.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_32521.png | 95.8 KB | ||
Filedesc metadata | emd-32521.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32521 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32521 | HTTPS FTP |
-Validation report
Summary document | emd_32521_validation.pdf.gz | 396.4 KB | Display | EMDB validaton report |
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Full document | emd_32521_full_validation.pdf.gz | 396 KB | Display | |
Data in XML | emd_32521_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_32521_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32521 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32521 | HTTPS FTP |
-Related structure data
Related structure data | 7wi4MC 7wi3C 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_32521.map.gz / Format: CCP4 / Size: 15.6 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: #1 |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-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 K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 70.795055 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 IFIDQIDAVG RQRGAGLGGG HDEREQTLNQ MLVEMDGFEG NEGIIVIAAT NRPDVLDPAL LRPGRFDRQV VVG LPDVRG REQILKVHMR RVPLAPDIDA AIIARGTPGF SGADLANLVN EAALFAARGN KRVVSMVEFE KAKDKIMMGA ERRS MVMTE AQKESTAYHQ 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 |
-Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 6 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32359 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |