6Q7M

Spiral structure of E. coli RavA in the RavA-LdcI cage-like complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex.

Jessop, M.Arragain, B.Miras, R.Fraudeau, A.Huard, K.Bacia-Verloop, M.Catty, P.Felix, J.Malet, H.Gutsche, I.

(2020) Commun Biol 3: 46-46

  • DOI: 10.1038/s42003-020-0772-0
  • Primary Citation of Related Structures:  

  • PubMed 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 inside the LdcI-RavA cage, RavA hexamers adopt an asymme ...

    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.


    Organizational Affiliation

    Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, CEA, CNRS, DRF, IRIG, UMR 5249, 17 rue des Martyrs, F-38054, Grenoble, France.,Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France. jan.felix@ibs.fr.,Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France. helene.malet@ibs.fr.,Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France. irina.gutsche@ibs.fr.,Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inducible lysine decarboxylase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
715Escherichia coli O157:H7Mutation(s): 0 
Gene Names: cadA (ldcI)
EC: 4.1.1.18
Find proteins for P0A9H4 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A9H4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATPase RavA
U, V, W, X, Y, Z
497Escherichia coliMutation(s): 0 
Gene Names: yieN (ravA)
EC: 3.6.3.-
Find proteins for J7QAN2 (Escherichia coli)
Go to UniProtKB:  J7QAN2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
V, W, X, Y, Z
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionFrance647784
Grenoble Instruct-ERIC CenterFranceUMS 3518 CNRS-CEA-UJF-EMBL
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-02
European Molecular Biology OrganizationFranceALTF441-2017

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-19
    Type: Database references