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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 | |||||||||
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![]() | RIBOSOME / Ribosomal assembly intermediate | |||||||||
Function / homology | ![]() mRNA N-acetyltransferase activity / perforant pathway to dendrate granule cell synapse / regulation of translation at postsynapse / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / snoRNA localization / leucine zipper domain binding / granular component / tRNA wobble cytosine modification ...mRNA N-acetyltransferase activity / perforant pathway to dendrate granule cell synapse / regulation of translation at postsynapse / U6 snRNA 2'-O-ribose methyltransferase activity / oocyte growth / nucleologenesis / snoRNA localization / leucine zipper domain binding / granular component / tRNA wobble cytosine modification / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / tRNA acetylation / U4atac snRNP / CURI complex / UTP-C complex / regulation of stem cell population maintenance / t-UTP complex / U4atac snRNA binding / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / negative regulation of amyloid precursor protein biosynthetic process / rRNA modification / pre-snoRNP complex / box C/D sno(s)RNA binding / preribosome / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / dense fibrillar component / histone methyltransferase binding / regulation of centrosome duplication / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / N-acetyltransferase activity / regulation of transcription elongation by RNA polymerase II / box C/D methylation guide snoRNP complex / positive regulation of rRNA processing / tRNA export from nucleus / cilium disassembly / embryonic cleavage / rRNA primary transcript binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / spindle assembly involved in female meiosis / blastocyst formation / epigenetic programming in the zygotic pronuclei / U4 snRNA binding / protein localization to nucleolus / Cul4-RING E3 ubiquitin ligase complex / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / rRNA methylation / telomerase holoenzyme complex / negative regulation of RNA splicing / box C/D snoRNP assembly / neural precursor cell proliferation / neural crest cell differentiation / U3 snoRNA binding / negative regulation of bicellular tight junction assembly / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / NRAGE signals death through JNK / protein acetylation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / rRNA metabolic process / positive regulation of transcription by RNA polymerase I / negative regulation of telomere maintenance via telomerase / Association of TriC/CCT with target proteins during biosynthesis / Protein hydroxylation / TOR signaling / SARS-CoV-1 modulates host translation machinery / RNA polymerase II complex binding / cellular response to ethanol / TFIID-class transcription factor complex binding / mTORC1-mediated signalling / Peptide chain elongation / negative regulation of apoptotic signaling pathway / Selenocysteine synthesis / decidualization / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / chromosome, centromeric region / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Vanden Broeck, A. / Singh, S. / Klinge, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 635 KB | Display | |
Data in CIF | ![]() | 1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 | ![]() 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]) |
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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) ![]() |
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#2: RNA chain | Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 70017.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: RNA chain | Mass: 4269.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#5: Protein | Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#45: Protein | Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: Protein | Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#63: Protein | Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() | ||||||
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#19: Protein | Mass: 74985.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | | Mass: 106248.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | | Mass: 105443.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #29: Protein | | Mass: 68189.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#35: Protein | Mass: 29483.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 127748.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 80431.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 66160.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: Protein | Mass: 59686.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#65: Protein | Mass: 68259.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#21: Protein | Mass: 76993.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#23: Protein | Mass: 70297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 62097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#64: Protein | Mass: 88129.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+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) ![]() |
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#32: Protein | Mass: 78988.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 33818.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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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: ![]() |
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: ![]() |
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
EM software |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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