[English] 日本語
Yorodumi
- PDB-6edo: Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6edo
TitleFull-length S. pombe Mdn1 in the presence of AMPPNP (ring region)
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 / 4 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 9, 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9032
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Midasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,3916
Polyers262,8601
Non-polymers2,5315
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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


Mass: 262860.312 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
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 5 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
Compound detailsWE ASSIGNED THE AA RESIDUES INTO THE EM DENSITY FOR THE RESIDUES 1-2147. HOWEVER, THE SEQUENCE ...WE ASSIGNED THE AA RESIDUES INTO THE EM DENSITY FOR THE RESIDUES 1-2147. HOWEVER, THE SEQUENCE ASSIGNMENT AND THE HELICAL REGISTRY OF THE OTHER RESIDUES WERE LEFT AMBIGUOUS (UNKS) EVEN THOUGH WE COULD TRACE THE CONNECTION OF THE EM DENSITY UP TO THE EDGE OF THE EM DENSITY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: N-terminal density map of the full-length Mdn1 in the presence of AMPPNP
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
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: GOLD / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 3000 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 88.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 8446
Image scansMovie frames/image: 50 / Used frames/image: 1-50

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2SerialEMimage acquisition
4CTFFIND4.1.5CTF correction
9RELION2.0.3initial Euler assignment
10FREALIGNfinal Euler assignment
11RELION2.0.3classification
12FREALIGN3D reconstruction
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 313336 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510120
ELECTRON MICROSCOPYf_angle_d0.92714050
ELECTRON MICROSCOPYf_dihedral_angle_d6.6275892
ELECTRON MICROSCOPYf_chiral_restr0.0481973
ELECTRON MICROSCOPYf_plane_restr0.0051961

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more