+Open data
-Basic information
Entry | Database: PDB / ID: 7mqa | |||||||||
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Title | Cryo-EM structure of the human SSU processome, state post-A1 | |||||||||
Components |
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Keywords | RIBOSOME / Ribosomal assembly intermediate | |||||||||
Function / homology | Function and homology information preribosome / U6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process ...preribosome / U6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / granular component / nuclear polyadenylation-dependent antisense transcript catabolic process / regulation of telomerase RNA localization to Cajal body / positive regulation of mRNA cis splicing, via spliceosome / RNA exonuclease activity / t-UTP complex / positive regulation of male gonad development / nuclear polyadenylation-dependent CUT catabolic process / CURI complex / UTP-C complex / TRAMP-dependent tRNA surveillance pathway / regulation of stem cell population maintenance / cytoplasmic exosome (RNase complex) / U4atac snRNP / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / U4atac snRNA binding / histone H2AQ104 methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-snoRNP complex / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (adenine-N6,N6-)-dimethyltransferase activity / box C/D sno(s)RNA binding / box C/D sno(s)RNA 3'-end processing / dense fibrillar component / histone mRNA catabolic process / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / histone methyltransferase binding / positive regulation of rRNA processing / regulation of transcription elongation by RNA polymerase II / tRNA export from nucleus / box C/D methylation guide snoRNP complex / spindle assembly involved in female meiosis / positive regulation of respiratory burst involved in inflammatory response / cilium disassembly / rRNA base methylation / nucleolus organization / epigenetic programming in the zygotic pronuclei / transcription elongation factor activity / Cul4-RING E3 ubiquitin ligase complex / rRNA primary transcript binding / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / U4 snRNA binding / protein localization to nucleolus / negative regulation of RNA splicing / telomerase RNA binding / SUMOylation of RNA binding proteins / RNA catabolic process / rRNA methylation / U2-type precatalytic spliceosome / U3 snoRNA binding / neural crest cell differentiation / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / maturation of 5.8S rRNA / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / Translation initiation complex formation / positive regulation of transcription by RNA polymerase I / fibroblast growth factor binding / mammalian oogenesis stage / activation-induced cell death of T cells / monocyte chemotaxis / RNA polymerase II complex binding / Protein hydroxylation / 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 / TFIID-class transcription factor complex binding / Selenocysteine synthesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Vanden Broeck, A. / Singh, S. / Klinge, S. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mqa.cif.gz | 5.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7mqa.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7mqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mqa_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7mqa_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7mqa_validation.xml.gz | 625.3 KB | Display | |
Data in CIF | 7mqa_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqa ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqa | HTTPS FTP |
-Related structure data
Related structure data | 23938MC 7mq8C 7mq9C 7mqjC M: map data used to model this data C: citing same article (ref.) |
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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
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules L0L1L2
#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: 604234.375 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 |
-40S ribosomal protein ... , 20 types, 20 molecules L3L4L5L6L7L8L9LALCLDLFLGNFNGNMNONPNQNUSR
#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 |
#35: Protein | Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277 |
#36: Protein | Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263 |
#40: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247 |
#41: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244 |
#42: Protein | Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019 |
#43: Protein | Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677 |
#47: Protein | Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708 |
#61: 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 ... , 6 types, 6 molecules LINDNHSASBST
#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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#34: Protein | Mass: 29483.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UMY1 |
#37: 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: 66160.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00567 |
#50: Protein | Mass: 59686.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2X3 |
#63: 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 |
#62: 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 , 26 types, 29 molecules LMLOLRLULYNBNINLNRNSNTNVSCSDSESFSGSHSISJSKSLSPSQSUSWSXSYSZ
-U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZNASM
#31: 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 |
#58: Protein | Mass: 33818.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96G21 |
-Non-polymers , 5 types, 71 molecules
#69: Chemical | ChemComp-MG / #70: Chemical | ChemComp-ATP / | #71: Chemical | #72: Chemical | ChemComp-GTP / | #73: 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 |
-Sample preparation
Component | Name: Human SSU processome / Type: RIBOSOME / Entity ID: #1-#68 / 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 |
-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 |
-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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459775 Details: 15 focused maps were reconstructed in RELION 3.1 and then assembled into a unique composite map using phenix.combine_focused_maps. Two half maps were generated using each half map from the focused refinement. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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