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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | SSU processome maturation and disassembly, State J | |||||||||
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Keywords | SSU processome / ribosome assembly / RNA folding / RNA-protein interactions / RIBOSOME | |||||||||
| Function / homology | Function and homology information18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / regulation of ribosomal protein gene transcription by RNA polymerase II / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / regulation of ribosomal protein gene transcription by RNA polymerase II / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / exosome (RNase complex) / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / t-UTP complex / nuclear exosome (RNase complex) / Pwp2p-containing subcomplex of 90S preribosome / snoRNA guided rRNA 2'-O-methylation / nuclear microtubule / Mpp10 complex / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (pseudouridine) methyltransferase activity / rRNA modification / histone H2AQ104 methyltransferase activity / septum digestion after cytokinesis / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA re-export from nucleus / histone mRNA catabolic process / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / nuclear mRNA surveillance / rRNA methyltransferase activity / rDNA heterochromatin / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / U4 snRNA binding / O-methyltransferase activity / SUMOylation of RNA binding proteins / protein localization to nucleolus / RNA catabolic process / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / regulation of telomere maintenance / U4 snRNP / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / poly(A)+ mRNA export from nucleus / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / proteasome assembly / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / 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) / U4/U6 x U5 tri-snRNP complex / ribosomal small subunit export from nucleus / RNA endonuclease activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Buzovetsky O / Klinge S | |||||||||
| Funding support | United States, 2 items
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Citation | Journal: To Be PublishedTitle: Mechanism of helicase-mediated SSU processome maturation and disassembly Authors: Buzovetsky O / Klinge S | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_49086.map.gz | 237.6 MB | EMDB map data format | |
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| Header (meta data) | emd-49086-v30.xml emd-49086.xml | 101.2 KB 101.2 KB | Display Display | EMDB header |
| Images | emd_49086.png | 154.8 KB | ||
| Filedesc metadata | emd-49086.cif.gz | 28.1 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-49086 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-49086 | HTTPS FTP |
-Validation report
| Summary document | emd_49086_validation.pdf.gz | 655.7 KB | Display | EMDB validaton report |
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| Full document | emd_49086_full_validation.pdf.gz | 655.6 KB | Display | |
| Data in XML | emd_49086_validation.xml.gz | 8 KB | Display | |
| Data in CIF | emd_49086_validation.cif.gz | 9.3 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-49086 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-49086 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9n76MC ![]() 9n6vC ![]() 9n6wC ![]() 9n6xC ![]() 9n6yC ![]() 9n6zC ![]() 9n70C ![]() 9n72C ![]() 9n73C ![]() 9n74C ![]() 9n75C ![]() 9n77C ![]() 9n78C ![]() 9n79C ![]() 9n7aC ![]() 9n7bC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_49086.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : SSU processome maturation and disassembly, State J
+Supramolecule #1: SSU processome maturation and disassembly, State J
+Macromolecule #1: 5'ETS rRNA
+Macromolecule #2: 18S rRNA
+Macromolecule #3: U3 snoRNA
+Macromolecule #4: 40S ribosomal protein S18-A
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S16-A
+Macromolecule #12: 40S ribosomal protein S11-A
+Macromolecule #13: 40S ribosomal protein S22-A
+Macromolecule #14: 40S ribosomal protein S24-A
+Macromolecule #15: 40S ribosomal protein S28-A
+Macromolecule #16: NET1-associated nuclear protein 1
+Macromolecule #17: U3 small nucleolar RNA-associated protein 8
+Macromolecule #18: U3 small nucleolar RNA-associated protein 15
+Macromolecule #19: U3 small nucleolar RNA-associated protein 9
+Macromolecule #20: U3 small nucleolar RNA-associated protein 5
+Macromolecule #21: U3 small nucleolar RNA-associated protein 10
+Macromolecule #22: U3 small nucleolar RNA-associated protein 4
+Macromolecule #23: Periodic tryptophan protein 2
+Macromolecule #24: U3 small nucleolar RNA-associated protein 6
+Macromolecule #25: U3 small nucleolar RNA-associated protein 12
+Macromolecule #26: U3 small nucleolar RNA-associated protein 13
+Macromolecule #27: U3 small nucleolar RNA-associated protein 18
+Macromolecule #28: U3 small nucleolar RNA-associated protein 21
+Macromolecule #29: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #30: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #31: Something about silencing protein 10
+Macromolecule #32: Bud site selection protein 21
+Macromolecule #33: 40S ribosomal protein S13
+Macromolecule #34: 40S ribosomal protein S14-A
+Macromolecule #35: U3 small nucleolar RNA-associated protein 22
+Macromolecule #36: Ribosomal RNA-processing protein 7
+Macromolecule #37: Dimethyladenosine transferase
+Macromolecule #38: Small ribosomal subunit protein eS1A
+Macromolecule #39: 40S ribosomal protein S19-A
+Macromolecule #40: 40S ribosomal protein S27-A
+Macromolecule #41: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #42: Exosome complex exonuclease RRP6
+Macromolecule #43: 40S ribosomal protein S12
+Macromolecule #44: Ubiquitin-40S ribosomal protein S31
+Macromolecule #45: Nucleolar protein 56
+Macromolecule #46: Nucleolar protein 58
+Macromolecule #47: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #48: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #49: Ribosomal RNA-processing protein 9
+Macromolecule #50: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #51: Ribosome biogenesis protein BMS1
+Macromolecule #52: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #53: rRNA-processing protein FCF1
+Macromolecule #54: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #55: U3 small nucleolar RNA-associated protein 20
+Macromolecule #56: rRNA-processing protein FCF2
+Macromolecule #57: 40S ribosomal protein S23-A
+Macromolecule #58: U3 small nucleolar RNA-associated protein 14
+Macromolecule #59: Nucleolar complex protein 14
+Macromolecule #60: Nucleolar complex protein 4
+Macromolecule #61: Regulator of rDNA transcription protein 14
+Macromolecule #62: Pre-rRNA-processing protein PNO1
+Macromolecule #63: U3 small nucleolar RNA-associated protein 11
+Macromolecule #64: Essential nuclear protein 1
+Macromolecule #65: MAGNESIUM ION
+Macromolecule #66: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #67: ZINC ION
+Macromolecule #68: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #69: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 Component:
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.6 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Authors
United States, 2 items
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Processing
FIELD EMISSION GUN
