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Yorodumi- EMDB-6616: State 2 of cryo-EM structure of the yeast pre-60S particles isola... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6616 | |||||||||
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Title | State 2 of cryo-EM structure of the yeast pre-60S particles isolated with Nog2-TAP | |||||||||
Map data | Reconstruction of pre-60S ribosome | |||||||||
Sample |
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Keywords | Pre-60S particle / ribosome biogenesis / assembly factor / Nog2 / Nog1 / ITS2 / Translation | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | Shan W / Beril K / Kaige Y / Hailey B / Yi XZ / Dan T / Michael G / Yi Y / Zhi FL / Jelena J ...Shan W / Beril K / Kaige Y / Hailey B / Yi XZ / Dan T / Michael G / Yi Y / Zhi FL / Jelena J / Cheng YM / Jian LL / Meng QD / Woolford Jr JL / Ning G | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Authors: Shan Wu / Beril Tutuncuoglu / Kaige Yan / Hailey Brown / Yixiao Zhang / Dan Tan / Michael Gamalinda / Yi Yuan / Zhifei Li / Jelena Jakovljevic / Chengying Ma / Jianlin Lei / Meng-Qiu Dong / ...Authors: Shan Wu / Beril Tutuncuoglu / Kaige Yan / Hailey Brown / Yixiao Zhang / Dan Tan / Michael Gamalinda / Yi Yuan / Zhifei Li / Jelena Jakovljevic / Chengying Ma / Jianlin Lei / Meng-Qiu Dong / John L Woolford / Ning Gao / Abstract: Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the ...Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6616.map.gz | 17.1 MB | EMDB map data format | |
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Header (meta data) | emd-6616-v30.xml emd-6616.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6616_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_6616.jpg | 97.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6616 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6616 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6616.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of pre-60S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : state2 of pre-60S ribosome subunit
Entire | Name: state2 of pre-60S ribosome subunit |
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Components |
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-Supramolecule #1000: state2 of pre-60S ribosome subunit
Supramolecule | Name: state2 of pre-60S ribosome subunit / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: pre-60S ribosome
Supramolecule | Name: pre-60S ribosome / type: complex / ID: 1 / Recombinant expression: Yes / Ribosome-details: ribosome-eukaryote: LSU 60S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy #1
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Microscopy ID | 1 |
Date | Nov 7, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #2
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Microscopy ID | 2 |
Date | Nov 22, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #3
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Microscopy ID | 3 |
Date | Apr 30, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |