PDB-6c0f: Yeast nucleolar pre-60S ribosomal subunit (state 2)

Basic information

• Entry: Database: PDB / ID: 6c0f
• Title: Yeast nucleolar pre-60S ribosomal subunit (state 2)

Components

• (60S ribosomal protein ...) x 19
• (Ribosomal RNA-processing protein ...) x 3
• (Ribosome biogenesis protein ...) x 7
• 5.8S rRNA
• ATP-dependent RNA helicase HAS1
• Brx1-associated peptide
• Eukaryotic translation initiation factor 6
• ITS2
• Nucleolar GTP-binding protein 1
• Nucleolar protein 16
• Pescadillo homolog
• Proteasome-interacting protein CIC1
• Protein MAK11
• Protein MAK16
• Ribosome production factor 1
• Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA
• rRNA-processing protein EBP2

• Keywords: RIBOSOME / Pre-60S / ribosome biogenesis / LSU processome

Function / homology

Function:

snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cell size / preribosome, small subunit precursor / proteasome binding / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / cell cycle / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol

Domain/homology:

Ribosomal protein L36 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3450 / translation elongation factor selb, chain A, domain 4 / Ribosomal RNA-processing protein 14, N-terminal / 60S ribosome biogenesis protein Rrp14 / Ribosomal RNA-processing protein 15 / Protein Peter Pan-like / Rrp15p / Surfeit locus 6 / Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain / Surfeit locus protein 6 / WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosomal protein L15e / Ribosomal protein L15 / Ribosome biogenesis protein 15, RNA recognition motif / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / U3 snoRNP protein/Ribosome production factor 1 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ubiquitin-like (UB roll) - #10 / Pescadillo / Pescadillo N-terminus / SH3 type barrels. - #30 / BRCT domain, a BRCA1 C-terminus domain / Ribosomal protein L30/S12 / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Brix domain / Brix domain / Brix domain profile. / Brix / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding domain / Translation factors / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / metallochaperone-like domain / TRASH domain / breast cancer carboxy-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein L6e

Component:

: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / Ribosomal RNA-processing protein 14 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Proteasome-interacting protein CIC1 / Ribosome biogenesis protein SSF1 / Ribosome production factor 1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Large ribosomal subunit protein eL37A / Ribosome biogenesis protein NSA1 / Pescadillo homolog / Ribosome biogenesis protein 15 / Large ribosomal subunit protein eL6A / Nucleolar GTP-binding protein 1 / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Ribosomal RNA-processing protein 15 / Ribosome biogenesis protein RLP24 / Ribosome biogenesis protein BRX1 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A

• Biological species: Saccharomyces cerevisiae BY4741 (yeast)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
• Authors: Sanghai, Z.A. / Miller, L. / Barandun, J. / Hunziker, M. / Chaker-Margot, M. / Klinge, S.

Funding support

United States, Switzerland, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	1DP2GM123459	United States
Swiss National Science Foundation	155515	Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM115327-Tan	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103314	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM109824	United States

• Citation: Journal: Nature / Year: 2018; Title: Modular assembly of the nucleolar pre-60S ribosomal subunit.; Authors: Zahra Assur Sanghai / Linamarie Miller / Kelly R Molloy / Jonas Barandun / Mirjam Hunziker / Malik Chaker-Margot / Junjie Wang / Brian T Chait / Sebastian Klinge / ; Abstract: Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.

History

Deposition	Dec 29, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization