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- EMDB-9063: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7 -

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Basic information

Entry
Database: EMDB / ID: EMD-9063
TitleCryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7
Map data
SampleAAA-ATPase Rix7:
Rix7 mutant / unknown protein / ligand
Function / homologyAAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / P-loop containing nucleoside triphosphate hydrolase / AAA ATPase, AAA+ lid domain / ATP binding / Uncharacterized protein
Function and homology information
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLo YH / Sobhany M / Hsu AL / Ford BL / Krahn JM / Borgnia MJ / Stanley RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7.
Authors: Yu-Hua Lo / Mack Sobhany / Allen L Hsu / Brittany L Ford / Juno M Krahn / Mario J Borgnia / Robin E Stanley /
Abstract: Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly ...Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly factors from pre-60S particles, but the mechanism of release is unknown. Rix7's mammalian homolog, NVL2 has been linked to cancer and mental illness disorders, highlighting the need to understand the molecular mechanisms of this essential machine. Here we report the cryo-EM reconstruction of the tandem AAA domains of Rix7 which form an asymmetric stacked homohexameric ring. We trapped Rix7 with a polypeptide in the central channel, revealing Rix7's role as a molecular unfoldase. The structure establishes that type II AAA-ATPases lacking the aromatic-hydrophobic motif within the first AAA domain can engage a substrate throughout the entire central channel. The structure also reveals that Rix7 contains unique post-α7 insertions within both AAA domains important for Rix7 function.
Validation ReportPDB-ID: 6mat

SummaryFull reportAbout validation report
History
DepositionAug 28, 2018-
Header (metadata) releaseSep 12, 2018-
Map releaseFeb 6, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mat
  • Surface level: 0.0796
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9063.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 192 pix.
= 266.88 Å
1.39 Å/pix.
x 192 pix.
= 266.88 Å
1.39 Å/pix.
x 192 pix.
= 266.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.0796 / Movie #1: 0.0796
Minimum - Maximum-0.14773183 - 0.31063178
Average (Standard dev.)0.0005223646 (±0.017758228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z266.880266.880266.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1480.3110.001

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Supplemental data

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Sample components

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Entire AAA-ATPase Rix7

EntireName: AAA-ATPase Rix7 / Number of components: 4

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Component #1: protein, AAA-ATPase Rix7

ProteinName: AAA-ATPase Rix7 / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Rix7 mutant

ProteinName: Rix7 mutant / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 89.418266 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, unknown protein

ProteinName: unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.315846 kDa
SourceSpecies: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: -1200.0 - -2700.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 64386
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Details: 5C18 was used for reference restraints in refinement
Input PDB model: 5FTK
Output model

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