- EMDB-23937: Cryo-EM structure of the human SSU processome, state pre-A1* -
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Basic information
Entry
Database: EMDB / ID: EMD-23937
Title
Cryo-EM structure of the human SSU processome, state pre-A1*
Map data
Local resolution filtered map
Sample
Complex: Human SSU processome
RNA: x 4 types
Protein or peptide: x 65 types
Ligand: x 5 types
Keywords
Ribosomal assembly intermediate / RIBOSOME
Function / homology
Function and homology information
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 / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA ...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 / 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 / sno(s)RNA-containing ribonucleoprotein complex / spindle assembly involved in female meiosis / rRNA base methylation / blastocyst formation / U4 snRNA binding / protein localization to nucleolus / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / telomerase holoenzyme complex / rRNA methylation / negative regulation of RNA splicing / box C/D snoRNP assembly / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neural precursor cell proliferation / neural crest cell differentiation / U3 snoRNA binding / negative regulation of bicellular tight junction 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 / precatalytic spliceosome / snoRNA binding / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / protein acetylation / NRAGE signals death through JNK / 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 / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / Peptide chain elongation / negative regulation of apoptotic signaling pathway / decidualization / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Maturation of protein E Similarity search - Function
Protein of unknown function DUF4602 / : / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / 40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / WDR36/Utp21 second beta-propeller domain ...Protein of unknown function DUF4602 / : / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / 40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / NUC153 / Nucleolar protein 10/Enp2 / : / : / NUC153 domain / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / rRNA-processing protein Fcf1, PIN domain / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / : / : / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / BING4CT (NUC141) domain / : / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Utp14 protein / UTP15 C terminal / rRNA-processing protein Fcf1/Utp23 / Sas10 C-terminal domain / Fcf1 / Sas10 C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / : / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 Similarity search - Domain/homology
U3 small nucleolar ribonucleoprotein protein MPP10 / Nucleolar protein 56 / WD repeat-containing protein 46 / U3 small nucleolar RNA-interacting protein 2 / Small subunit processome component 20 homolog / Small ribosomal subunit protein eS17 / rRNA 2'-O-methyltransferase fibrillarin / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 ...U3 small nucleolar ribonucleoprotein protein MPP10 / Nucleolar protein 56 / WD repeat-containing protein 46 / U3 small nucleolar RNA-interacting protein 2 / Small subunit processome component 20 homolog / Small ribosomal subunit protein eS17 / rRNA 2'-O-methyltransferase fibrillarin / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / NHP2-like protein 1 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Transducin beta-like protein 3 / KRR1 small subunit processome component homolog / Ribosome biogenesis protein BMS1 homolog / WD repeat-containing protein 43 / Periodic tryptophan protein 2 homolog / Deoxynucleotidyltransferase terminal-interacting protein 2 / WD repeat-containing protein 75 / 40S small subunit processome assembly factor 1 / WD repeat-containing protein 36 / U3 small nucleolar RNA-associated protein 15 homolog / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 4 homolog / U3 small nucleolar ribonucleoprotein protein IMP4 / Nucleolar protein 10 / U3 small nucleolar RNA-associated protein 14 homolog A / RNA cytidine acetyltransferase / HEAT repeat-containing protein 1 / Nucleolar protein 6 / Something about silencing protein 10 / RNA-binding protein PNO1 / DDB1- and CUL4-associated factor 13 / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein AATF / U3 small nucleolar RNA-associated protein 6 homolog / U3 small nucleolar RNA-associated protein NOL7 / WD repeat-containing protein 3 / RNA 3'-terminal phosphate cyclase-like protein / Nucleolar protein 58 / rRNA-processing protein FCF1 homolog / Probable U3 small nucleolar RNA-associated protein 11 / Ribosomal RNA-processing protein 7 homolog A / U3 small nucleolar RNA-associated protein 18 homolog Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.87 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
1DP2GM123459
United States
European Molecular Biology Organization (EMBO)
ALTF 711-2019
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
Deposition
May 5, 2021
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Header (metadata) release
Sep 22, 2021
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Map release
Sep 22, 2021
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Update
May 29, 2024
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Current status
May 29, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: RNA cytidine acetyltransferase / type: protein_or_peptide / ID: 35 / Number of copies: 2 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Model: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
Vitrification
Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number real images: 84904 / Average electron dose: 58.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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