|Entry||Database: PDB / ID: 6q7m|
|Title||Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex|
|Keywords||HYDROLASE / Complex / MoxR ATPase / Lysine decarboxylase|
|Function / homology|
Function and homology information
lysine decarboxylase activity / lysine decarboxylase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / cellular amino acid metabolic process / ATPase-coupled transmembrane transporter activity / ATPase activity / ATP binding / cytoplasm
Ornithine/lysine/arginine decarboxylase / Pyridoxal phosphate-dependent transferase / ATPase RavA-like, AAA lid domain / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATPase RavA / ATPase, RavA, C-terminal / Orn/Lys/Arg decarboxylase, major domain / AAA+ ATPase domain / Orn/Lys/Arg decarboxylase, N-terminal ...Ornithine/lysine/arginine decarboxylase / Pyridoxal phosphate-dependent transferase / ATPase RavA-like, AAA lid domain / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATPase RavA / ATPase, RavA, C-terminal / Orn/Lys/Arg decarboxylase, major domain / AAA+ ATPase domain / Orn/Lys/Arg decarboxylase, N-terminal / Orn/Lys/Arg decarboxylase, C-terminal / ATPase, dynein-related, AAA domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase domain 1
ATPase RavA / Inducible lysine decarboxylase
|Biological species||Escherichia coli (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å|
|Authors||Arragain, B. / Felix, J. / Malet, H. / Gutsche, I. / Jessop, M.|
|Funding support|| France, 4items |
|Citation||Journal: Commun Biol / Year: 2020|
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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Inducible lysine decarboxylase
B: Inducible lysine decarboxylase
C: Inducible lysine decarboxylase
D: Inducible lysine decarboxylase
E: Inducible lysine decarboxylase
F: Inducible lysine decarboxylase
G: Inducible lysine decarboxylase
H: Inducible lysine decarboxylase
I: Inducible lysine decarboxylase
J: Inducible lysine decarboxylase
K: Inducible lysine decarboxylase
L: Inducible lysine decarboxylase
M: Inducible lysine decarboxylase
N: Inducible lysine decarboxylase
O: Inducible lysine decarboxylase
P: Inducible lysine decarboxylase
Q: Inducible lysine decarboxylase
R: Inducible lysine decarboxylase
S: Inducible lysine decarboxylase
T: Inducible lysine decarboxylase
U: ATPase RavA
V: ATPase RavA
W: ATPase RavA
X: ATPase RavA
Y: ATPase RavA
Z: ATPase RavA
Mass: 81357.008 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cadA, ldcI, Z5734, ECs5113 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9H4, lysine decarboxylase
Mass: 56351.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yieN, ravA, BN17_37001 / Production host: Escherichia coli (E. coli)
References: UniProt: J7QAN2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Complex of the hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI.|
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
|Molecular weight||Value: 3.3 MDa|
|Source (natural)||Organism: Escherichia coli (E. coli)|
|Source (recombinant)||Organism: Escherichia coli (E. coli) / Strain: MG1655 delta_relA delta_spoT|
|Buffer solution||pH: 7.9 |
Details: 20 mM Tris pH 7.9, 300 mM NaCl, 2 mM ADP, 10 mM MgCl 2 , 0.1 mM PLP and 1 mM DTT
|Specimen||Conc.: 0.98 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
Details: Concentrations of LdcI and RavA were 0.38 mg/ml (4.67 microM) and 0.6 mg/ml (10.64 microM) respectively.
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Microscopy||Model: 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 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 41270 X|
|Image recording||Average exposure time: 8 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1819|
|Image scans||Movie frames/image: 40 / Used frames/image: 3-40|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 18902 |
Details: The cleanded dataset contains 11866 particles. Dataset expansion (C5) resulted in a dataset containing 59330 particles.
|Symmetry||Point symmetry: C1 (asymmetric)|
|3D reconstruction||Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16513 / Num. of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Protocol: FLEXIBLE FIT|
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.
|Atomic model building|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi