+Open data
-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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Function / homology | Function and homology information preribosome / nucleolar exosome (RNase complex) / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process ...preribosome / nucleolar exosome (RNase complex) / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / granular component / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / regulation of telomerase RNA localization to Cajal body / TRAMP-dependent tRNA surveillance pathway / positive regulation of male gonad development / CUT catabolic process / RNA exonuclease activity / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / U4atac snRNP / nuclear polyadenylation-dependent rRNA catabolic process / regulation of stem cell population maintenance / CURI complex / UTP-C complex / t-UTP complex / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / U4atac snRNA binding / rRNA (pseudouridine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / histone H2AQ104 methyltransferase activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-snoRNP complex / box C/D sno(s)RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / dense fibrillar component / nuclear mRNA surveillance / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / histone methyltransferase binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription elongation by RNA polymerase II / positive regulation of rRNA processing / tRNA export from nucleus / positive regulation of respiratory burst involved in inflammatory response / epigenetic programming in the zygotic pronuclei / cilium disassembly / nucleolus organization / spindle assembly involved in female meiosis / transcription elongation factor activity / rRNA base methylation / rRNA primary transcript binding / blastocyst formation / Cul4-RING E3 ubiquitin ligase complex / protein localization to nucleolus / RNA splicing, via transesterification reactions / U4 snRNA binding / negative regulation of RNA splicing / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SUMOylation of RNA binding proteins / RNA catabolic process / rRNA methylation / telomerase RNA binding / U2-type precatalytic spliceosome / neural crest cell differentiation / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Cajal body / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / Translation initiation complex formation / snoRNA binding / precatalytic spliceosome / mammalian oogenesis stage / activation-induced cell death of T cells / maturation of 5.8S rRNA / positive regulation of transcription by RNA polymerase I / fibroblast growth factor binding / Protein hydroxylation / RNA polymerase II complex binding / monocyte chemotaxis / Association of TriC/CCT with target proteins during biosynthesis / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (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: 2021 Title: 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. | |||||||||
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_23938.map.gz | 619.1 MB | EMDB map data format | |
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Header (meta data) | emd-23938-v30.xml emd-23938.xml | 118.9 KB 118.9 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 | |
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 | 842.5 KB | Display | EMDB validaton report |
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Full document | emd_23938_full_validation.pdf.gz | 842 KB | Display | |
Data in XML | emd_23938_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | emd_23938_validation.cif.gz | 37.6 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 (ref.) 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 processome Data 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-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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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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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_23938_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_23938_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_23938_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 |
-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: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-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 |