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- EMDB-0369: Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0369 | ||||||||||||||||||
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Title | Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit | ||||||||||||||||||
![]() | Cryo-EM structure of late nuclear pre-60S ribosomal subunit | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Zhou Y / Musalgaonkar S / Johnson AW / Taylor DW | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Authors: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor / ![]() Abstract: The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the ...The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 201.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 64.9 KB 64.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.5 KB | Display | ![]() |
Images | ![]() | 185.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n8jMC ![]() 0370C ![]() 0371C ![]() 0372C ![]() 0373C ![]() 0374C ![]() 6n8kC ![]() 6n8lC ![]() 6n8mC ![]() 6n8nC ![]() 6n8oC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of late nuclear pre-60S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Late nuclear (LN) pre-60S ribosomal subunit
+Supramolecule #1: Late nuclear (LN) pre-60S ribosomal subunit
+Macromolecule #1: 60S ribosomal protein L5
+Macromolecule #2: 60S ribosomal protein L11-A
+Macromolecule #3: 60S ribosomal protein L2-A
+Macromolecule #4: 60S ribosomal protein L28
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: Nucleolar GTP-binding protein 1
+Macromolecule #7: 60S ribosomal protein L4-A
+Macromolecule #8: 60S ribosomal protein L30
+Macromolecule #9: 60S ribosomal protein L31-A
+Macromolecule #10: 60S ribosomal protein L6-A
+Macromolecule #11: 60S ribosomal protein L32
+Macromolecule #12: 60S ribosomal protein L7-A
+Macromolecule #13: 60S ribosomal protein L33-A
+Macromolecule #14: 60S ribosomal protein L8-A
+Macromolecule #15: 60S ribosomal protein L34-A
+Macromolecule #16: Bud site selection protein 20
+Macromolecule #17: 60S ribosomal protein L9-A
+Macromolecule #18: 60S ribosomal protein L35-A
+Macromolecule #19: 60S ribosomal protein L36-A
+Macromolecule #20: 60S ribosomal protein L37-A
+Macromolecule #21: 60S ribosomal protein L38
+Macromolecule #22: Nucleolar GTP-binding protein 2
+Macromolecule #23: 60S ribosomal protein L13-A
+Macromolecule #24: 60S ribosomal protein L39
+Macromolecule #25: 60S ribosomal protein L14-A
+Macromolecule #26: 60S ribosomal protein L43-A
+Macromolecule #27: 60S ribosomal protein L15-A
+Macromolecule #28: Ribosome biogenesis protein RLP24
+Macromolecule #29: 60S ribosomal protein L16-A
+Macromolecule #30: 60S ribosomal protein L17-A
+Macromolecule #31: 60S ribosomal protein L18-A
+Macromolecule #32: 60S ribosomal protein L19-A
+Macromolecule #33: Ribosome biogenesis protein NSA2
+Macromolecule #34: 60S ribosomal protein L20-A
+Macromolecule #35: 60S ribosomal protein L21-A
+Macromolecule #36: 60S ribosomal protein L22-A
+Macromolecule #37: 60S ribosomal protein L23-A
+Macromolecule #38: Ribosome assembly factor MRT4
+Macromolecule #39: 60S ribosomal protein L25
+Macromolecule #40: 60S ribosomal protein L26-A
+Macromolecule #41: Eukaryotic translation initiation factor 6
+Macromolecule #42: 60S ribosomal protein L27-A
+Macromolecule #43: UPF0642 protein YBL028C
+Macromolecule #44: 60S ribosomal protein L12
+Macromolecule #45: 60S ribosomal protein L42-A
+Macromolecule #46: 60S ribosomal protein L29
+Macromolecule #47: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #48: 5S rRNA
+Macromolecule #49: 5.8S rRNA
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |