[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleCryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.
Journal, issue, pagesNat. Struct. Mol. Biol., Vol. 26, Issue 9, Page 830-839, Year 2019
Publish dateSep 5, 2019
AuthorsMonica C Pillon / Allen L Hsu / Juno M Krahn / Jason G Williams / Kevin H Goslen / Mack Sobhany / Mario J Borgnia / Robin E Stanley /
PubMed AbstractRibosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The ...Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 assemble into a multienzyme complex, herein designated RNase PNK, to orchestrate processing of precursor ribosomal RNA (rRNA). RNase PNK belongs to the functionally diverse HEPN nuclease superfamily, whose members rely on distinct cues for nuclease activation. To establish how RNase PNK coordinates its dual enzymatic activities, we solved a series of cryo-EM structures of Chaetomium thermophilum RNase PNK in multiple conformational states. The structures reveal that RNase PNK adopts a butterfly-like architecture, harboring a composite HEPN nuclease active site flanked by discrete RNA kinase sites. We identify two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish a new mechanism of HEPN nuclease activation essential for ribosome production.
External linksPubMed:31488907 / Publisher's page
KeywordsCatalytic Domain / Chaetomium / Cryoelectron Microscopy / Fungal Proteins / Multienzyme Complexes / Protein Conformation / RNA Precursors / RNA BINDING PROTEIN / Complex / Ribonuclease / Polynucleotide kinase
MethodsEM (single particle)
Resolution2.9 - 3.2 A
Structure data

EMDB-20040:
Precursor ribosomal RNA processing complex, State 2.

EMDB-20041:
Precursor ribosomal RNA processing complex, State 1.

EMDB-20042:
Precursor ribosomal RNA processing complex, apo-state.

PDB-6of2:
Precursor ribosomal RNA processing complex, State 2.

PDB-6of3:
Precursor ribosomal RNA processing complex, State 1.

PDB-6of4:
Precursor ribosomal RNA processing complex, apo-state.

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
MAGNESIUM ION / Magnesium

Source
  • Chaetomium thermophilum (fungus)
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)

+
About EMN Papers

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

  • Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.
    PageDataFormat
    EMN Searchsearch resultCSV, TSV, or JSON
    EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Feb 20, 2018. PDBj/BINDS workshop in Osaka University

PDBj/BINDS workshop in Osaka University

    Read more

    -
    EMN Papers

    Database of articles cited by 3DEM data entries

    • Database of articles cited by 3DEM data entries in EMDB and PDB
    • Using PubMed data

    Related info.:EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

    Read more