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- EMDB-9036: Full-length S. pombe Mdn1 in the presence of ATP and Rbin-1 -

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Basic information

Entry
Database: EMDB / ID: 9036
TitleFull-length S. pombe Mdn1 in the presence of ATP and Rbin-1
Map dataFull-length S. pombe Mdn1 in the presence of ATP and Rbin-1, primary map
SampleFull-length Mdn1 in the presence of ATP and Rbin-1:
Function / homologyvon Willebrand factor, type A / ATPase, dynein-related, AAA domain / VWFA domain profile. / AAA domain (dynein-related subfamily) / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Midasin / AAA+ ATPase domain / preribosome, large subunit precursor / rRNA processing ...von Willebrand factor, type A / ATPase, dynein-related, AAA domain / VWFA domain profile. / AAA domain (dynein-related subfamily) / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Midasin / AAA+ ATPase domain / preribosome, large subunit precursor / rRNA processing / ribosomal large subunit assembly / ATPase activity / nucleolus / calcium ion binding / nucleoplasm / ATP binding / Midasin
Function and homology information
SourceSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / 7.2 Å resolution
AuthorsChen Z / Suzuki H / Wang AC / DiMaio F / Walz T / Kapoor TM
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.
Authors: Zhen Chen / Hiroshi Suzuki / Yuki Kobayashi / Ashley C Wang / Frank DiMaio / Shigehiro A Kawashima / Thomas Walz / Tarun M Kapoor
Abstract: Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 ...Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 amino acid [aa]) and its limited homology to other well-studied proteins have restricted our understanding of its remodeling function. Here, we present structures for S. pombe Mdn1 in the presence of AMPPNP at up to ∼4 Å or ATP plus Rbin-1, a chemical inhibitor, at ∼8 Å resolution. These data reveal that Mdn1's MIDAS domain is tethered to its ring-shaped AAA domain through an ∼20 nm long structured linker and a flexible ∼500 aa Asp/Glu-rich motif. We find that the MIDAS domain, which also binds other ribosome-assembly factors, docks onto the AAA ring in a nucleotide state-specific manner. Together, our findings reveal how conformational changes in the AAA ring can be directly transmitted to the MIDAS domain and thereby drive the targeted release of assembly factors from ribosomal 60S-subunit precursors.
Validation ReportPDB-ID: 6ees

SummaryFull reportAbout validation report
DateDeposition: Aug 9, 2018 / Header (metadata) release: Aug 29, 2018 / Map release: Oct 17, 2018 / Last update: Oct 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ees
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

Fileemd_9036.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.5 Å/pix.
= 384. Å
256 pix
1.5 Å/pix.
= 384. Å
256 pix
1.5 Å/pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.043622382 - 0.11560972
Average (Standard dev.)0.00057838415 (0.004665724)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 384.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0440.1160.001

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Supplemental data

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Sample components

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Entire Full-length Mdn1 in the presence of ATP and Rbin-1

EntireName: Full-length Mdn1 in the presence of ATP and Rbin-1 / Number of components: 1

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Component #1: cellular-component, Full-length Mdn1 in the presence of ATP and Rbin-1

Cellular-componentName: Full-length Mdn1 in the presence of ATP and Rbin-1 / Recombinant expression: No
MassTheoretical: 540 kDa
SourceSpecies: Schizosaccharomyces pombe (fission yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 66.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 28000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3887

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 54557
3D reconstructionSoftware: RELION / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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