+Open data
-Basic information
Entry | Database: PDB / ID: 7mq9 | |||||||||
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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 information mRNA N-acetyltransferase activity / negative regulation of superoxide anion generation / preribosome / 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 / negative regulation of superoxide anion generation / preribosome / 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 / tRNA wobble cytosine modification / U4atac snRNP / CURI complex / regulation of stem cell population maintenance / negative regulation of amyloid precursor protein biosynthetic process / t-UTP complex / UTP-C 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 / tRNA export from nucleus / 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 / transcription elongation factor activity / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / rRNA primary transcript binding / cilium disassembly / blastocyst formation / rRNA base methylation / Cul4-RING E3 ubiquitin ligase complex / RNA splicing, via transesterification reactions / negative regulation of RNA splicing / sno(s)RNA-containing ribonucleoprotein complex / N-acetyltransferase activity / protein localization to nucleolus / response to stimulus / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP complex / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / neural crest cell differentiation / rRNA methylation / box C/D snoRNP 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 / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / mammalian oogenesis stage / snoRNA binding / intercellular bridge / activation-induced cell death of T cells / NRAGE signals death through JNK / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / protein acetylation / Protein hydroxylation / RNA polymerase II complex binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / TFIID-class transcription factor complex binding / Eukaryotic Translation Termination / blastocyst development / negative regulation of apoptotic signaling pathway / negative regulation of telomere maintenance via telomerase / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / decidualization / Viral mRNA Translation / ubiquitin-like ligase-substrate adaptor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 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 | 7mq9.cif.gz | 5.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7mq9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7mq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mq9_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7mq9_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7mq9_validation.xml.gz | 583.3 KB | Display | |
Data in CIF | 7mq9_validation.cif.gz | 995.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/7mq9 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mq9 | HTTPS FTP |
-Related structure data
Related structure data | 23937MC 7mq8C 7mqaC 7mqjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 603757.500 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 |
#62: RNA chain | Mass: 7197.572 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) |
#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 |
#33: Protein | Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277 |
#34: Protein | Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263 |
#36: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247 |
#38: Protein | Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244 |
#39: Protein | Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677 |
#42: Protein | Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708 |
#54: 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 #23: Protein | | Mass: 106248.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNX4 #25: Protein | | Mass: 105443.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NI36 #27: 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 LINDNWSASBNHST
#17: Protein | Mass: 75231.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#31: Protein | Mass: 29483.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UMY1 |
#43: Protein | Mass: 80431.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSC4 |
#44: Protein | Mass: 66160.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00567 |
#45: Protein | Mass: 59686.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2X3 |
#58: Protein | Mass: 127748.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6R4 |
#66: 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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#20: Protein | Mass: 76993.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969X6 |
#22: Protein | Mass: 70297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYH9 |
#24: Protein | Mass: 62097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5J1 |
#55: 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, 30 molecules LOLUNBNENJNKNNNRNTSCSDSESFSHSISKSJSLSQSXSYSPLRLMSGNISWSUNYSZ
-U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZNASM
#28: 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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#29: Protein | Mass: 78988.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00566 |
#52: 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, 30 molecules
#70: Chemical | ChemComp-MG / #71: Chemical | #72: Chemical | ChemComp-GTP / | #73: Chemical | #74: 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-#69 / 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: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21096 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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