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Open data
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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 informationmRNA cytidine N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / nucleologenesis / oocyte growth / snoRNA localization / granular component / leucine zipper domain binding / tRNA wobble cytosine modification / U4atac snRNP / U4atac snRNA binding ...mRNA cytidine N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / nucleologenesis / oocyte growth / snoRNA localization / granular component / leucine zipper domain binding / tRNA wobble cytosine modification / U4atac snRNP / U4atac snRNA binding / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / regulation of stem cell population maintenance / tRNA acetylation / CURI complex / UTP-C complex / pre-snoRNP complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / box C/D sno(s)RNA binding / Mpp10 complex / negative regulation of amyloid precursor protein biosynthetic process / rRNA modification / rRNA (pseudouridine) methyltransferase activity / histone H2AQ104 methyltransferase activity / rRNA 2'-O-methylation / dense fibrillar component / histone methyltransferase binding / box C/D sno(s)RNA 3'-end processing / preribosome / 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 / regulation of centrosome duplication / N-acetyltransferase activity / 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 / tRNA export from nucleus / embryonic cleavage / positive regulation of rRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA splicing, via transesterification reactions / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / blastocyst formation / rRNA base methylation / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / protein localization to nucleolus / rRNA methylation / telomerase holoenzyme complex / U4 snRNA binding / box C/D snoRNP assembly / transcription elongation factor activity / spindle assembly involved in female meiosis / neural precursor cell proliferation / epigenetic programming in the zygotic pronuclei / protein acetylation / negative regulation of RNA splicing / U3 snoRNA binding / mRNA modification / neural crest cell differentiation / NRAGE signals death through JNK / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / precatalytic spliceosome / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / snoRNA binding / preribosome, small subunit precursor / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / negative regulation of bicellular tight junction assembly / rRNA metabolic process / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / decidualization / blastocyst development / Cul4-RING E3 ubiquitin ligase complex / positive regulation of transcription by RNA polymerase I / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / Ribosomal scanning and start codon recognition / spliceosomal complex assembly / Translation initiation complex formation / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / spliceosomal tri-snRNP complex assembly / Protein hydroxylation / TOR signaling / negative regulation of apoptotic signaling pathway / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / cellular response to ethanol / Peptide chain elongation / chromosome, centromeric region / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator 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: 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_23936.map.gz | 615.5 MB | EMDB map data format | |
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| Header (meta data) | emd-23936-v30.xml emd-23936.xml | 125.6 KB 125.6 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 |
-Related structure data
| Related structure data | ![]() 7mq8MC ![]() 7mq9C ![]() 7mqaC ![]() 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_23936.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_23936_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_23936_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_23936_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_23936_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 #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 peptide
+Macromolecule #69: Unassigned peptides
+Macromolecule #70: Probable U3 small nucleolar RNA-associated protein 11
+Macromolecule #71: Bystin
+Macromolecule #72: MAGNESIUM ION
+Macromolecule #73: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #74: ZINC ION
+Macromolecule #75: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #76: 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-7mq8: |
Movie
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About Yorodumi



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







































































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



































































