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Open data
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Basic information
| Entry | Database: EMDB / ID: EMD-23938 | |||||||||
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| Title | Cryo-EM structure of the human SSU processome, state post-A1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosomal assembly intermediate / RIBOSOME | |||||||||
| Function / homology | Function and homology informationU6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / positive regulation of mRNA cis splicing, via spliceosome / snoRNA localization / granular component / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / RNA exonuclease activity ...U6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / positive regulation of mRNA cis splicing, via spliceosome / snoRNA localization / granular component / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / RNA exonuclease activity / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / regulation of telomerase RNA localization to Cajal body / positive regulation of male gonad development / U4atac snRNP / CUT catabolic process / regulation of stem cell population maintenance / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent CUT catabolic process / U4atac snRNA binding / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / CURI complex / UTP-C complex / pre-snoRNP complex / 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 / 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 / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / preribosome / rRNA (adenine-N6,N6-)-dimethyltransferase activity / histone mRNA catabolic process / dense fibrillar component / histone methyltransferase binding / box C/D sno(s)RNA 3'-end processing / nuclear mRNA surveillance / rRNA methyltransferase activity / 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) / regulation of transcription elongation by RNA polymerase II / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cilium disassembly / box C/D methylation guide snoRNP complex / positive regulation of rRNA processing / tRNA export from nucleus / RNA splicing, via transesterification reactions / transcription elongation factor activity / positive regulation of respiratory burst involved in inflammatory response / rRNA primary transcript binding / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / nucleolus organization / rRNA base methylation / U4 snRNA binding / SUMOylation of RNA binding proteins / protein localization to nucleolus / U2-type precatalytic spliceosome / telomerase RNA binding / spindle assembly involved in female meiosis / negative regulation of RNA splicing / epigenetic programming in the zygotic pronuclei / RNA catabolic process / rRNA methylation / box C/D snoRNP assembly / neural crest cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / neural precursor cell proliferation / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / Cul4-RING E3 ubiquitin ligase complex / Translation initiation complex formation / rRNA metabolic process / fibroblast growth factor binding / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / monocyte chemotaxis / positive regulation of transcription by RNA polymerase I / TOR signaling / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / decidualization / RNA polymerase II complex binding / TFIID-class transcription factor complex binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Vanden Broeck A / Singh S / Klinge S | |||||||||
| Funding support | United States, 2 items
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Citation | Journal: Science / Year: 2021Title: Nucleolar maturation of the human small subunit processome. Authors: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge / ![]() Abstract: The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution ...The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within. | |||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
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Downloads & links
-EMDB archive
| Map data | emd_23938.map.gz | 619.1 MB | EMDB map data format | |
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| Header (meta data) | emd-23938-v30.xml emd-23938.xml | 126.5 KB 126.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_23938_fsc.xml | 19.7 KB | Display | FSC data file |
| Images | emd_23938.png | 163.1 KB | ||
| Masks | emd_23938_msk_1.map | 669.9 MB | Mask map | |
| Filedesc metadata | emd-23938.cif.gz | 31.3 KB | ||
| Others | emd_23938_additional_1.map.gz emd_23938_half_map_1.map.gz emd_23938_half_map_2.map.gz | 616.4 MB 536.2 MB 536.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23938 | HTTPS FTP |
-Validation report
| Summary document | emd_23938_validation.pdf.gz | 1009.8 KB | Display | EMDB validaton report |
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| Full document | emd_23938_full_validation.pdf.gz | 1009.4 KB | Display | |
| Data in XML | emd_23938_validation.xml.gz | 27.8 KB | Display | |
| Data in CIF | emd_23938_validation.cif.gz | 37.7 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23938 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23938 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7mqaMC ![]() 7mq8C ![]() 7mq9C ![]() 7mqjC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | |
| EM raw data | EMPIAR-10781 (Title: Nucleolar maturation of the human small subunit processomeData size: 74.6 TB Data #1: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 2 [micrographs - multiframe] Data #3: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 3 [micrographs - multiframe] Data #4: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 4 [micrographs - multiframe] Data #5: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 5 [micrographs - multiframe] Data #6: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 6 [micrographs - multiframe] Data #7: Aligned and averaged micrographs of human SSU processomes - Dataset 1 [micrographs - single frame] Data #8: Aligned and averaged micrographs of human SSU processomes - Dataset 2 [micrographs - single frame] Data #9: Aligned and averaged micrographs of human SSU processomes - Dataset 3 [micrographs - single frame] Data #10: Aligned and averaged micrographs of human SSU processomes - Dataset 4 [micrographs - single frame] Data #11: Aligned and averaged micrographs of human SSU processomes - Dataset 5 [micrographs - single frame] Data #12: Aligned and averaged micrographs of human SSU processomes - Dataset 6 [micrographs - single frame]) |
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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_23938.map.gz / Format: CCP4 / Size: 669.9 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
| File | emd_23938_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_23938_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_23938_half_map_1.map | ||||||||||||
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-Half map: #1
| File | emd_23938_half_map_2.map | ||||||||||||
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Sample components
+Entire : Human SSU processome
+Supramolecule #1: Human SSU processome
+Macromolecule #1: 5'ETS rRNA
+Macromolecule #2: 18S rRNA
+Macromolecule #3: U3 snoRNA
+Macromolecule #4: 40S ribosomal protein S18
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6
+Macromolecule #8: 40S ribosomal protein S7
+Macromolecule #9: 40S ribosomal protein S8
+Macromolecule #10: 40S ribosomal protein S9
+Macromolecule #11: 40S ribosomal protein S12
+Macromolecule #12: 40S ribosomal protein S16
+Macromolecule #13: 40S ribosomal protein S11
+Macromolecule #14: 40S ribosomal protein S24
+Macromolecule #15: 40S ribosomal protein S28
+Macromolecule #16: WD repeat-containing protein 75
+Macromolecule #17: Nucleolar protein 11
+Macromolecule #18: U3 small nucleolar RNA-associated protein 15 homolog
+Macromolecule #19: WD repeat-containing protein 43
+Macromolecule #20: HEAT repeat-containing protein 1
+Macromolecule #21: U3 small nucleolar RNA-associated protein 4 homolog
+Macromolecule #22: Periodic tryptophan protein 2 homolog
+Macromolecule #23: U3 small nucleolar RNA-associated protein 6 homolog
+Macromolecule #24: WD repeat-containing protein 3
+Macromolecule #25: Transducin beta-like protein 3
+Macromolecule #26: U3 small nucleolar RNA-associated protein 18 homolog
+Macromolecule #27: WD repeat-containing protein 36
+Macromolecule #28: DDB1- and CUL4-associated factor 13
+Macromolecule #29: WD repeat-containing protein 46
+Macromolecule #30: Active regulator of SIRT1
+Macromolecule #31: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #32: U3 small nucleolar ribonucleoprotein protein MPP10
+Macromolecule #33: Something about silencing protein 10
+Macromolecule #34: Nucleolar protein 7
+Macromolecule #35: 40S ribosomal protein S13
+Macromolecule #36: 40S ribosomal protein S14
+Macromolecule #37: Nucleolar protein 6
+Macromolecule #38: Ribosomal RNA-processing protein 7 homolog A
+Macromolecule #39: Probable dimethyladenosine transferase
+Macromolecule #40: 40S ribosomal protein S3a
+Macromolecule #41: 40S ribosomal protein S15a
+Macromolecule #42: 40S ribosomal protein S19
+Macromolecule #43: 40S ribosomal protein S27
+Macromolecule #44: RRP12-like protein
+Macromolecule #45: Probable ATP-dependent RNA helicase DHX37
+Macromolecule #46: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #47: 40S ribosomal protein S17
+Macromolecule #48: Exosome component 10
+Macromolecule #49: Nucleolar protein 56
+Macromolecule #50: Nucleolar protein 58
+Macromolecule #51: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #52: NHP2-like protein 1
+Macromolecule #53: U3 small nucleolar RNA-interacting protein 2
+Macromolecule #54: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #55: Ribosome biogenesis protein BMS1 homolog
+Macromolecule #56: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #57: rRNA-processing protein FCF1 homolog
+Macromolecule #58: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #59: Small subunit processome component 20 homolog
+Macromolecule #60: Deoxynucleotidyltransferase terminal-interacting protein 2
+Macromolecule #61: 40S ribosomal protein S23
+Macromolecule #62: U3 small nucleolar RNA-associated protein 14 homolog A
+Macromolecule #63: Nucleolar protein 14
+Macromolecule #64: Nucleolar complex protein 4 homolog
+Macromolecule #65: RNA-binding protein PNO1
+Macromolecule #66: Unassigned peptides
+Macromolecule #67: Probable U3 small nucleolar RNA-associated protein 11
+Macromolecule #68: Bystin
+Macromolecule #69: MAGNESIUM ION
+Macromolecule #70: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #71: ZINC ION
+Macromolecule #72: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #73: S-ADENOSYL-L-HOMOCYSTEINE
-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: 7.6 |
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| Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Specialist optics | Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 84904 / Average electron dose: 58.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model |
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| Refinement | Space: REAL | ||||||||||||||||||||||||
| Output model | ![]() PDB-7mqa: |
Movie
Controller
About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 2 items
Citation
UCSF Chimera













































































Z (Sec.)
Y (Row.)
X (Col.)





































































