Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 29, Issue 12, Page 1228-1238, Year 2022
Publish date	Dec 8, 2022
Authors	Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger /
PubMed Abstract	DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.
External links	Nat Struct Mol Biol / PubMed:36482249 / PubMed Central
Methods	EM (single particle)
Resolution	2.76 - 3.71 Å
Structure data	24269 7nac EMDB-24269: State E2 nucleolar 60S ribosomal biogenesis intermediate - Overall map PDB-7nac: State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Method: EM (single particle) / Resolution: 3.04 Å 24270 7nad EMDB-24270, PDB-7nad: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model Method: EM (single particle) / Resolution: 3.04 Å 24271 7naf EMDB-24271: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD locally refined map PDB-7naf: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model Method: EM (single particle) / Resolution: 3.13 Å 24280 7r6k EMDB-24280: State E2 nucleolar 60S ribosomal intermediate - Local Map for Noc2/Noc3 region PDB-7r6k: State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Method: EM (single particle) / Resolution: 3.17 Å 24286 7r6q EMDB-24286: State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region map PDB-7r6q: State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Method: EM (single particle) / Resolution: 2.98 Å 24290 7r72 EMDB-24290: State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 locally refined map PDB-7r72: State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model Method: EM (single particle) / Resolution: 3.07 Å 24296 7r7a EMDB-24296, PDB-7r7a: State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Method: EM (single particle) / Resolution: 3.04 Å 24297 7r7c EMDB-24297: State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local map PDB-7r7c: State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model Method: EM (single particle) / Resolution: 3.71 Å 26259 7u0h EMDB-26259: State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall map PDB-7u0h: State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Method: EM (single particle) / Resolution: 2.76 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine ChemComp-HOH: WATER / Water ChemComp-MG: Unknown entry
Source	saccharomyces cerevisiae by4741 (yeast)
Keywords	RIBOSOME / ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / methyltransferases / DEAD-box ATPase