+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23936 | |||||||||
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Title | Cryo-EM structure of the human SSU processome, state pre-A1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosomal assembly intermediate / RIBOSOME | |||||||||
Function / homology | Function and homology information mRNA N-acetyltransferase activity / preribosome / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / leucine zipper domain binding / snoRNA localization / granular component / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity ...mRNA N-acetyltransferase activity / preribosome / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / leucine zipper domain binding / snoRNA localization / granular component / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / U4atac snRNP / regulation of stem cell population maintenance / CURI complex / UTP-C complex / negative regulation of amyloid precursor protein biosynthetic process / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / U4atac snRNA binding / rRNA (pseudouridine) methyltransferase activity / rRNA modification / histone H2AQ104 methyltransferase activity / 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) / dense fibrillar component / regulation of centrosome duplication / 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 / embryonic cleavage / tRNA export from nucleus / epigenetic programming in the zygotic pronuclei / cilium disassembly / 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 / N-acetyltransferase activity / 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 / telomerase holoenzyme complex / rRNA methylation / 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 / 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 / intercellular bridge / precatalytic spliceosome / mammalian oogenesis stage / NRAGE signals death through JNK / protein acetylation / activation-induced cell death of T cells / positive regulation of transcription by RNA polymerase I / Protein hydroxylation / RNA polymerase II complex binding / regulation of mitotic cell cycle / 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 / TFIID-class transcription factor complex binding / Formation of a pool of free 40S subunits / negative regulation of telomere maintenance via telomerase / Eukaryotic Translation Termination / blastocyst development / ubiquitin ligase inhibitor activity / negative regulation of apoptotic signaling pathway / decidualization / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / chromosome, centromeric region / Viral mRNA Translation / condensed nuclear chromosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_23936.map.gz | 615.5 MB | EMDB map data format | |
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Header (meta data) | emd-23936-v30.xml emd-23936.xml | 124.5 KB 124.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23936_fsc.xml | 19.8 KB | Display | FSC data file |
Images | emd_23936.png | 161 KB | ||
Masks | emd_23936_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-23936.cif.gz | 31.4 KB | ||
Others | emd_23936_additional_1.map.gz emd_23936_half_map_1.map.gz emd_23936_half_map_2.map.gz | 614.3 MB 535 MB 534.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23936 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23936 | HTTPS FTP |
-Validation report
Summary document | emd_23936_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_23936_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_23936_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | emd_23936_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23936 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23936 | HTTPS FTP |
-Related structure data
Related structure data | 7mq8MC 7mq9C 7mqaC 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_23936.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_23936_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_23936_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_23936_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_23936_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 #31: 5'ETS rRNA
+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: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #32: U3 small nucleolar ribonucleoprotein protein MPP10
+Macromolecule #33: Something about silencing protein 10
+Macromolecule #34: Neuroguidin
+Macromolecule #35: Nucleolar protein 7
+Macromolecule #36: Uncharacterized protein C1orf131
+Macromolecule #37: 40S ribosomal protein S13
+Macromolecule #38: 40S ribosomal protein S14
+Macromolecule #39: Nucleolar protein 6
+Macromolecule #40: Ribosomal RNA-processing protein 7 homolog A
+Macromolecule #41: RNA cytidine acetyltransferase
+Macromolecule #42: 40S ribosomal protein S3a
+Macromolecule #43: Protein AATF
+Macromolecule #44: 40S ribosomal protein S15a
+Macromolecule #45: 40S ribosomal protein S27
+Macromolecule #46: RRP12-like protein
+Macromolecule #47: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #48: 40S ribosomal protein S17
+Macromolecule #49: Nucleolar protein 10
+Macromolecule #50: KRR1 small subunit processome component homolog
+Macromolecule #51: Nucleolar protein 56
+Macromolecule #52: Nucleolar protein 58
+Macromolecule #53: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #54: NHP2-like protein 1
+Macromolecule #55: U3 small nucleolar RNA-interacting protein 2
+Macromolecule #56: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #57: Ribosome biogenesis protein BMS1 homolog
+Macromolecule #58: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #59: rRNA-processing protein FCF1 homolog
+Macromolecule #60: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #61: Small subunit processome component 20 homolog
+Macromolecule #62: Deoxynucleotidyltransferase terminal-interacting protein 2
+Macromolecule #63: 40S ribosomal protein S23
+Macromolecule #64: U3 small nucleolar RNA-associated protein 14 homolog A
+Macromolecule #65: Nucleolar protein 14
+Macromolecule #66: Nucleolar complex protein 4 homolog
+Macromolecule #67: RNA-binding protein PNO1
+Macromolecule #68: Unassigned peptides
+Macromolecule #69: Probable U3 small nucleolar RNA-associated protein 11
+Macromolecule #70: Bystin
+Macromolecule #71: MAGNESIUM ION
+Macromolecule #72: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #73: ZINC ION
+Macromolecule #74: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #75: 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||||||||||||||
Output model | PDB-7mq8: |