- EMDB-3888: State A (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway o... -
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Basic information
Entry
Database: EMDB / ID: EMD-3888
Title
State A (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Map data
Visualizing the assembly pathway of nucleolar pre-60S ribosmes - StateA (Nsa1-TAP Flag-Ytm1)
Sample
Complex: Large subunit biogenesis particle purified via Nsa1-TAP and Flag-Ytm1
Function / homology
Function and homology information
snoRNA release from pre-rRNA / nuclear division / 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 / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...snoRNA release from pre-rRNA / nuclear division / 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 / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / proteasome binding / 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 / 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) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / 90S preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome complex / nuclear periphery / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / protein catabolic process / ribosomal large subunit assembly / rRNA processing / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / nuclear envelope / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / cell cycle / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain ...WDR74/Nsa1 / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / Ribosome biogenesis protein 15, RNA recognition motif / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / 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 / U3 snoRNP protein/Ribosome production factor 1 / Pescadillo / Pescadillo N-terminus / BRCT domain, a BRCA1 C-terminus domain / Brix domain / Brix domain / Brix domain profile. / Brix / 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. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / breast cancer carboxy-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal Protein L6, KOW domain / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein L32e, conserved site / Ribosomal protein L7A/L8 / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L14, KOW motif / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal L30 N-terminal domain / Ribosomal protein L14 / 60S ribosomal protein L4 C-terminal domain / 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 L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L32e / Ribosomal protein L32e superfamily / 60S ribosomal protein L35 / Ribosomal_L32e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L32 / Ribosomal protein L35A / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L32e signature. / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / BRCT domain profile. / Ribosomal protein L1e signature. / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / BRCT domain / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L37ae/L37e Similarity search - Domain/homology
Large ribosomal subunit protein eL36B / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A ...Large ribosomal subunit protein eL36B / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / rRNA-processing protein EBP2 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Proteasome-interacting protein CIC1 / 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 / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Ribosome biogenesis protein BRX1 / Large ribosomal subunit protein eL13A Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 4.2 Å
Journal: Cell / Year: 2017 Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann / Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
History
Deposition
Sep 29, 2017
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Header (metadata) release
Nov 15, 2017
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Map release
Dec 27, 2017
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Update
Dec 27, 2017
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Current status
Dec 27, 2017
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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