6Q7L

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 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:  
    6Q7L, 6Q7M, 6SZA, 6SZB

  • 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 asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations ...

    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

    Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France. irina.gutsche@ibs.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inducible lysine decarboxylase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
715Escherichia coliMutation(s): 0 
Gene Names: cadAldcIZ5734ECs5113
EC: 4.1.1.18
UniProt
Find proteins for P0A9H4 (Escherichia coli O157:H7)
Explore P0A9H4 
Go to UniProtKB:  P0A9H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9H4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase RavAU498Escherichia coliMutation(s): 0 
Gene Names: ravAyieNb3746JW3725
EC: 3.6.3
UniProt
Find proteins for P31473 (Escherichia coli (strain K12))
Explore P31473 
Go to UniProtKB:  P31473
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UniProt GroupP31473
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase RavAV, W, X, Y, Z497Escherichia coliMutation(s): 0 
Gene Names: yieNravABN17_37001
EC: 3.6.3
UniProt
Find proteins for J7QAN2 (Escherichia coli)
Explore J7QAN2 
Go to UniProtKB:  J7QAN2
Entity Groups  
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UniProt GroupJ7QAN2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
UA [auth V],
VA [auth W],
WA [auth X],
XA [auth Y],
YA [auth Z]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth B],
CA [auth C],
DA [auth D],
EA [auth E],
AA [auth A],
BA [auth B],
CA [auth C],
DA [auth D],
EA [auth E],
FA [auth F],
GA [auth G],
HA [auth H],
IA [auth I],
JA [auth J],
KA [auth K],
LA [auth L],
MA [auth M],
NA [auth N],
OA [auth O],
PA [auth P],
QA [auth Q],
RA [auth R],
SA [auth S],
TA [auth T]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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  (Full details and data files)

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