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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: 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 / ATPase family associated with various cellular activities (AAA) / AAA-protein family signature. / ATP binding / Uncharacterized protein
Function and homology information
SourceChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsLo YH / Sobhany M / Hsu AL / Ford BL / Krahn JM / Borgnia MJ / Stanley RE
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
Validation ReportPDB-ID: 6mat

SummaryFull reportAbout validation report
DateDeposition: Aug 28, 2018 / Header (metadata) release: Sep 12, 2018 / Map release: Feb 6, 2019 / Last update: Feb 13, 2019

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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
  • Map surface with fitted models
  • 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

Fileemd_9063.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.39 Å/pix.
= 266.88 Å
192 pix
1.39 Å/pix.
= 266.88 Å
192 pix
1.39 Å/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 Level:0.0796 (by author), 0.0796 (movie #1):
Minimum - Maximum-0.14773183 - 0.31063178
Average (Standard dev.)0.0005223646 (0.017758228)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 266.88 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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: 4 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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