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- PDB-6ees: Fitted model of S. pombe Mdn1 into the cryo-EM map obtained in th... -

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Basic information

Entry
Database: PDB / ID: 6ees
TitleFitted model of S. pombe Mdn1 into the cryo-EM map obtained in the presence of ATP and Rbin-1
ComponentsMidasin
KeywordsMOTOR PROTEIN / Ribosome biogenesis / AAA protein / Mechanochemical enzyme / Ribosome assembly factor
Function / homologyMidasin AAA lid domain / ATPase, dynein-related, AAA domain / Midasin AAA lid 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 / von Willebrand factor, type A ...Midasin AAA lid domain / ATPase, dynein-related, AAA domain / Midasin AAA lid 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 / von Willebrand factor, type A / preribosome, large subunit precursor / rRNA processing / ribosomal large subunit assembly / ATPase activity / nucleolus / calcium ion binding / nucleoplasm / ATP binding / Midasin
Function and homology information
Specimen sourceSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.7 Å resolution
AuthorsChen, Z. / Suzuki, H. / Wang, A.C. / DiMaio, F. / Walz, T. / Kapoor, T.M.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Aug 15, 2018 / Release: Oct 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 17, 2018Structure modelrepositoryInitial release
1.1Oct 31, 2018Structure modelData collection / Database referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
A: Midasin


Theoretical massNumber of molelcules
Total (without water)284,5561
Polyers284,5561
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Midasin / Dynein-related AAA-ATPase mdn1 / MIDAS-containing protein


Mass: 284556.188 Da / Num. of mol.: 1
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mdn1, SPCC737.08 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94248

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full-length Mdn1 in the presence of ATP and Rbin-1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 28000 / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 66.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3887
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1.5CTF correction
7UCSF Chimeramodel fitting
9RELION2.0.3initial Euler assignment
10RELION2.0.3final Euler assignment
11RELION2.0.3classification
12RELION2.0.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 54557 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 6EDO
Pdb chain ID: A / Pdb chain residue range: 2-2383

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