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- EMDB-4469: Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4469 | |||||||||||||||
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Title | Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex | |||||||||||||||
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![]() | Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI.: Inducible lysine decarboxylase / (ATPase RavA) x 2 / (ligand ![]() | |||||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Arragain B / Felix J / Malet H / Gutsche I / Jessop M | |||||||||||||||
Funding support | ![]()
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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. | |||||||||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Others |
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Archive directory |
-Related structure data
Related structure data | ![]() 6q7lCM ![]() 4470C ![]() 6q7mC ![]() 6szaC ![]() 6szbC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 2.42 Å / Y: 2.42 Å / Z: 2.42001 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Unfiltered half-map 1.
File | emd_4469_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map 2.
File | emd_4469_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric ...
+Component #1: protein, Complex of the hexameric MoxR AAA+ ATPase RavA and the d...
+Component #2: protein, Inducible lysine decarboxylase
+Component #3: protein, ATPase RavA
+Component #4: protein, ATPase RavA
+Component #5: ligand, PYRIDOXAL-5'-PHOSPHATE
+Component #6: ligand, ADENOSINE-5'-DIPHOSPHATE
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | Specimen conc.: 0.98 mg/mL Buffer solution: 20 mM Tris pH 7.9, 300 mM NaCl, 2 mM ADP, 10 mM MgCl 2 , 0.1 mM PLP and 1 mM DTT pH: 7.9 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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![]() | Microscope: FEI POLARA 300 Details: Data collection was performed on an FEI Polara microscope operated at 300 kV. Movies of 40 frames were collected with a total exposure time of 8s and a total dose of 40e-/Angstrom^2 on a K2 ...Details: Data collection was performed on an FEI Polara microscope operated at 300 kV. Movies of 40 frames were collected with a total exposure time of 8s and a total dose of 40e-/Angstrom^2 on a K2 summit direct electron detector (Gatan) at a magnification of 41270x, corresponding to 1.21 Angstrom/pixel at the specimen level. |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 41270 X (calibrated) / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 1819 |
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Image processing
-Atomic model buiding
Modeling #1 | Refinement protocol: flexible Details: Local resolution estimation and subsequent filtering of maps were performed in Relion3.0. For fitting of atomic models in the resulting filtered maps, we used the previously-determined X-ray ...Details: Local resolution estimation and subsequent filtering of maps were performed in Relion3.0. For fitting of atomic models in the resulting filtered maps, we used the previously-determined X-ray structures of LdcI (PDB ID: 3N75) (Kanjee et al., 2011) and RavA (PDB ID: 3NBX) (El Bakkouri et al., 2010). In each map, two decameric LdcI molecules extracted from PDB 3N75 and one spiral RavA hexamer extracted from a continuous RavA helix generated from PDB 3NBX were fitted separately using iMODFIT (Lopez-Blanco and Chacon, 2013), followed by a single round of B-factor (ADP) refinement in Phenix. Input PDB model: 3N75, 3NBX |
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Output model |