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- EMDB-10351: MoxR AAA-ATPase RavA, C2-symmetric closed ring conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-10351
TitleMoxR AAA-ATPase RavA, C2-symmetric closed ring conformation
Map dataMoxR AAA-ATPase RavA, C2-symmetric closed ring conformation
Sample
  • Complex: RavA + Mg-ADP
    • Protein or peptide: RavA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ ATPase / MoxR / Escherichia coli / CHAPERONE
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems ...: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems / ATPase, RavA, LARA domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsJessop M / Felix J
Funding support1 items
OrganizationGrant numberCountry
European Research Council
CitationJournal: 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.
History
DepositionOct 2, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sza
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10351.png

Downloads & links

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Map

FileDownload / File: emd_10351.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMoxR AAA-ATPase RavA, C2-symmetric closed ring conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 256 pix.
= 309.76 Å		1.21 Å/pix.
x 256 pix.
= 309.76 Å		1.21 Å/pix.
x 256 pix.
= 309.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.50369245 - 1.5750815
Average (Standard dev.)0.0051131924 (±0.05230029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 309.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z309.760309.760309.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5041.5750.005

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Supplemental data

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Sample components

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Entire : RavA + Mg-ADP

EntireName: RavA + Mg-ADP
Components
  • Complex: RavA + Mg-ADP
    • Protein or peptide: RavA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: RavA + Mg-ADP

SupramoleculeName: RavA + Mg-ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 336 KDa

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Macromolecule #1: RavA

MacromoleculeName: RavA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 56.454586 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1072000
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3nbx


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6sza:
MoxR AAA-ATPase RavA, C2-symmetric closed ring conformation

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