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Open data
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Basic information
| Entry | Database: PDB / ID: 7mq8 | |||||||||
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| Title | Cryo-EM structure of the human SSU processome, state pre-A1 | |||||||||
Components |
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Keywords | RIBOSOME / Ribosomal assembly intermediate | |||||||||
| Function / homology | Function and homology informationmRNA N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / snoRNA localization / leucine zipper domain binding / granular component / tRNA wobble cytosine modification / U4atac snRNP / tRNA cytidine N4-acetyltransferase activity ...mRNA N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / snoRNA localization / leucine zipper domain binding / granular component / tRNA wobble cytosine modification / U4atac snRNP / 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 / U4atac snRNA binding / CURI complex / UTP-C complex / negative regulation of amyloid precursor protein biosynthetic process / pre-snoRNP complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / box C/D sno(s)RNA binding / rRNA modification / histone H2AQ104 methyltransferase activity / preribosome / dense fibrillar component / histone methyltransferase binding / box C/D sno(s)RNA 3'-end processing / 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 centrosome duplication / regulation of transcription elongation by RNA polymerase II / 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 / embryonic cleavage / positive regulation of rRNA processing / tRNA export from nucleus / RNA splicing, via transesterification reactions / rRNA primary transcript binding / transcription elongation factor activity / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / rRNA base methylation / SUMOylation of RNA binding proteins / U4 snRNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / protein localization to nucleolus / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / rRNA methylation / box C/D snoRNP assembly / negative regulation of RNA splicing / neural precursor cell proliferation / U3 snoRNA binding / neural crest cell differentiation / negative regulation of bicellular tight junction assembly / protein acetylation / rRNA modification in the nucleus and cytosol / precatalytic spliceosome / erythrocyte homeostasis / NRAGE signals death through JNK / preribosome, small subunit precursor / snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / Cul4-RING E3 ubiquitin ligase complex / negative regulation of ubiquitin protein ligase activity / rRNA metabolic process / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of transcription by RNA polymerase I / negative regulation of telomere maintenance via telomerase / decidualization / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / TOR signaling / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / negative regulation of apoptotic signaling pathway / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / chromosome, centromeric region / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / blastocyst development / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Vanden Broeck, A. / Singh, S. / Klinge, S. | |||||||||
| Funding support | United States, 2items
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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
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7mq8.cif.gz | 5.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7mq8.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7mq8.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/7mq8 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mq8 | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 23936MC ![]() 7mq9C ![]() 7mqaC ![]() 7mqjC M: map data used to model this data C: citing same article ( |
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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
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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Components
-RNA chain , 4 types, 4 molecules L0L1L2N0
| #1: RNA chain | Mass: 1166881.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1212788588 |
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| #2: RNA chain | Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227 |
| #3: RNA chain | Mass: 70017.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 37551 |
| #31: RNA chain | Mass: 4269.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-40S ribosomal protein ... , 19 types, 19 molecules L3L4L5L6L7L8L9LALCLDLFLGNFNGNMNONQNUSR
| #4: Protein | Mass: 12671.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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| #5: Protein | Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701 |
| #6: Protein | Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782 |
| #7: Protein | Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753 |
| #8: Protein | Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081 |
| #9: Protein | Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241 |
| #10: Protein | Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781 |
| #11: Protein | Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398 |
| #12: Protein | Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249 |
| #13: Protein | Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280 |
| #14: Protein | Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847 |
| #15: Protein | Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857 |
| #37: Protein | Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277 |
| #38: Protein | Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263 |
| #42: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247 |
| #44: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244 |
| #45: Protein | Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677 |
| #48: Protein | Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708 |
| #63: Protein | Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266 |
-WD repeat-containing protein ... , 5 types, 6 molecules LHLKLLLQLTLW
| #16: Protein | Mass: 94609.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IWA0 | ||||||
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| #19: Protein | Mass: 74985.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15061#24: Protein | | Mass: 106248.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNX4#27: Protein | | Mass: 105443.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NI36#29: Protein | | Mass: 68189.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15213 |
-Nucleolar protein ... , 7 types, 7 molecules LINDNHNWSASBST
| #17: Protein | Mass: 73444.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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| #35: Protein | Mass: 29483.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UMY1 |
| #39: Protein | Mass: 127748.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6R4 |
| #49: Protein | Mass: 80431.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSC4 |
| #51: Protein | Mass: 66160.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00567 |
| #52: Protein | Mass: 59686.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2X3 |
| #65: Protein | Mass: 68259.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-U3 small nucleolar RNA-associated protein ... , 5 types, 5 molecules LJLNLPLSSS
| #18: Protein | Mass: 58503.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TED0 |
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| #21: Protein | Mass: 76993.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969X6 |
| #23: Protein | Mass: 70297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYH9 |
| #26: Protein | Mass: 62097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5J1 |
| #64: Protein | Mass: 88129.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVJ6 |
+Protein , 27 types, 31 molecules LMLOLRLUNBNCNENINJNKNNNRNTNYSCSDSESFSGSHSISJSKSLSPSQSUSWSXSYSZ
-U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZNASM
| #30: Protein | Mass: 21889.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NV31 |
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| #32: Protein | Mass: 78988.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00566 |
| #60: Protein | Mass: 33818.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96G21 |
-Protein/peptide , 1 types, 1 molecules Sx
| #68: Protein/peptide | Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Non-polymers , 5 types, 30 molecules 








| #72: Chemical | ChemComp-MG / #73: Chemical | #74: Chemical | #75: Chemical | ChemComp-GTP / | #76: Chemical | |
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-Details
| Has ligand of interest | N |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: Human SSU processome / Type: RIBOSOME / Entity ID: #1-#30, #32-#67, #70-#71 / Source: NATURAL |
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| Molecular weight | Value: 5 MDa / Experimental value: NO |
| Source (natural) | Organism: Homo sapiens (human) |
| Buffer solution | pH: 7.6 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm |
| Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 84904 |
| EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 9297626 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42142 Details: 15 focused maps were reconstructed and post processed in relion and assembled in one unique composite map using phenix.resolve_cryo_em Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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About Yorodumi




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











































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