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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 / 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 / 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 / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ubiquitin-like ligase-substrate adaptor activity / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling 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
Arichive directory | ![]() ![]() | 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 | ![]() 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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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) ![]() |
-Non-polymers , 5 types, 30 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/SAH.gif)
#71: Chemical | ChemComp-MG / #72: Chemical | #73: Chemical | #74: Chemical | ChemComp-GTP / | #75: 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-#70 / 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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