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- EMDB-24269: State E2 nucleolar 60S ribosomal biogenesis intermediate - Overall map -
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Open data
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Basic information
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Title | State E2 nucleolar 60S ribosomal biogenesis intermediate - Overall map | ||||||||||||
![]() | Overall map of Spb1-MTD containing subset | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
Function / homology | ![]() 25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / 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) / rRNA (uridine-2'-O-)-methyltransferase activity ...25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / 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) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / nuclear pre-replicative complex / tRNA methylation / rRNA primary transcript binding / rRNA base methylation / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / protein folding chaperone complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / DNA replication initiation / mRNA transport / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor activity / proteasome complex / nuclear periphery / 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 / transcription corepressor activity / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / histone binding / 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 division / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
![]() | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Authors: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger / ![]() ![]() ![]() 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. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 265.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 89.2 KB 89.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 163.6 KB | ||
Filedesc metadata | ![]() | 20.3 KB | ||
Others | ![]() ![]() | 247.6 MB 252.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nacMC ![]() 7nadC ![]() 7nafC ![]() 7r6kC ![]() 7r6qC ![]() 7r72C ![]() 7r7aC ![]() 7r7cC ![]() 7u0hC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | Overall map of Spb1-MTD containing subset | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 1 of Spb1-MTD containing subset
File | emd_24269_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 of Spb1-MTD containing subset | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 of Spb1-MTD containing subset
File | emd_24269_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 of Spb1-MTD containing subset | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+Supramolecule #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #52: 5.8S ribosomal RNA gene and internal transcribed spacer 2
+Macromolecule #3: 60S ribosomal subunit assembly/export protein LOC1
+Macromolecule #4: Ribosome biogenesis protein BRX1
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L6-A
+Macromolecule #8: 60S ribosomal protein L7-A
+Macromolecule #9: 60S ribosomal protein L9-A
+Macromolecule #10: rRNA-processing protein EBP2
+Macromolecule #11: 60S ribosomal protein L13-A
+Macromolecule #12: 60S ribosomal protein L14-A
+Macromolecule #13: 60S ribosomal protein L15-A
+Macromolecule #14: 60S ribosomal protein L16-A
+Macromolecule #15: 60S ribosomal protein L17-A
+Macromolecule #16: 60S ribosomal protein L18-A
+Macromolecule #17: 60S ribosomal protein L20-A
+Macromolecule #18: 60S ribosomal protein L21-A
+Macromolecule #19: Ribosome assembly factor MRT4
+Macromolecule #20: 60S ribosomal protein L25
+Macromolecule #21: 60S ribosomal protein L26-A
+Macromolecule #22: Nucleolar GTP-binding protein 1
+Macromolecule #23: 60S ribosomal protein L31-A
+Macromolecule #24: 60S ribosomal protein L32
+Macromolecule #25: 60S ribosomal protein L33-A
+Macromolecule #26: 60S ribosomal protein L35-A
+Macromolecule #27: 60S ribosomal protein L36-A
+Macromolecule #28: 60S ribosomal protein L37-A
+Macromolecule #29: 60S ribosome subunit biogenesis protein NIP7
+Macromolecule #30: Ribosome biogenesis protein ERB1
+Macromolecule #31: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #32: Ribosome biogenesis protein NSA2
+Macromolecule #33: Nuclear GTP-binding protein NUG1
+Macromolecule #34: Ribosome biogenesis protein RLP24
+Macromolecule #35: Nucleolar protein 16
+Macromolecule #36: Eukaryotic translation initiation factor 6
+Macromolecule #37: UPF0642 protein YBL028C
+Macromolecule #38: NOC2 isoform 1
+Macromolecule #39: Nucleolar complex-associated protein 3
+Macromolecule #40: Proteasome-interacting protein CIC1
+Macromolecule #41: 60S ribosomal protein L23-A
+Macromolecule #42: 60S ribosomal protein L19-A
+Macromolecule #43: 60S ribosomal protein L8-A
+Macromolecule #44: 60S ribosomal protein L27-A
+Macromolecule #45: 60S ribosomal protein L22-A
+Macromolecule #46: 60S ribosomal protein L30
+Macromolecule #47: 60S ribosomal protein L34-A
+Macromolecule #48: 60S ribosomal protein L38
+Macromolecule #49: Pescadillo homolog
+Macromolecule #50: YTM1 isoform 1
+Macromolecule #51: Ribosome biogenesis protein RLP7
+Macromolecule #53: ATP-dependent RNA helicase HAS1
+Macromolecule #54: Ribosome biogenesis protein 15
+Macromolecule #55: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #56: Ribosomal protein
+Macromolecule #57: RRP17 isoform 1
+Macromolecule #58: ATP-dependent rRNA helicase SPB4
+Macromolecule #59: ZINC ION
+Macromolecule #60: S-ADENOSYL-L-HOMOCYSTEINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.45 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4523 / Average exposure time: 0.05 sec. / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7nac: |