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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10352 | |||||||||
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Title | MoxR AAA-ATPase RavA, spiral open ring conformation | |||||||||
![]() | MoxR AAA-ATPase RavA, spiral open ring conformation | |||||||||
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![]() | AAA+ ATPase / MoxR / ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jessop M / Felix J | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Authors: Matthew Jessop / Benoit Arragain / Roger Miras / Angélique Fraudeau / Karine Huard / Maria Bacia-Verloop / Patrice Catty / Jan Felix / Hélène Malet / Irina Gutsche / ![]() Abstract: The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that ...The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 123.8 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6szbMC ![]() 4469C ![]() 4470C ![]() 6q7lC ![]() 6q7mC ![]() 6szaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | MoxR AAA-ATPase RavA, spiral open ring conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : RavA + Mg-ADP
Entire | Name: RavA + Mg-ADP |
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Components |
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-Supramolecule #1: RavA + Mg-ADP
Supramolecule | Name: RavA + Mg-ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 336 KDa |
-Macromolecule #1: RavA + Mg-ADP
Macromolecule | Name: RavA + Mg-ADP / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 56.454586 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAHPHLLAER ISRLSSSLEK GLYERSHAIR LCLLAALSGE SVFLLGPPGI AKSLIARRLK FAFQNARAFE YLMTRFSTPE EVFGPLSIQ ALKDEGRYER LTSGYLPEAE IVFLDEIWKA GPAILNTLLT AINERQFRNG AHVEKIPMRL LVAASNELPE A DSSLEALY ...String: MAHPHLLAER ISRLSSSLEK GLYERSHAIR LCLLAALSGE SVFLLGPPGI AKSLIARRLK FAFQNARAFE YLMTRFSTPE EVFGPLSIQ ALKDEGRYER LTSGYLPEAE IVFLDEIWKA GPAILNTLLT AINERQFRNG AHVEKIPMRL LVAASNELPE A DSSLEALY DRMLIRLWLD KVQDKANFRS MLTSQQDEND NPVPDALQVT DEEYERWQKE IGEITLPDHV FELIFMLRQQ LD KLPDAPY VSDRRWKKAI RLLQASAFFS GRSAVAPVDL ILLKDCLWYD AQSLNLIQQQ IDVLMTGHAW QQQGMLTRLG AIV QRHLQL QQQQSDKTAL TVIRLGGIFS RRQQYQLPVN VTASTLTLLL QKPLKLHDME VVHISFERSA LEQWLSKGGE IRGK LNGIG FAQKLNLEVD SAQHLVVRDV SLQGSTLALP GSSAEGLPGE IKQQLEELES DWRKQHALFS EQQKCLFIPG DWLGR IEAS LQDVGAQIRQ AQQC UniProtKB: ATPase RavA |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |