7WTS image
Deposition Date 2022-02-05
Release Date 2022-10-19
Last Version Date 2024-06-26
Entry Detail
PDB ID:
7WTS
Keywords:
Title:
Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: 2)
Chain Length:1873
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Probable dimethyladenosine transferase
Gene (Uniprot):DIMT1
Chain IDs:W (auth: 3)
Chain Length:313
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 14 homolog A
Gene (Uniprot):UTP14A
Chain IDs:V (auth: 5)
Chain Length:771
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:C (auth: B)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:D (auth: E)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:G
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:F (auth: H)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:Q (auth: I)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:P (auth: J)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:RRP12-like protein
Gene (Uniprot):RRP12
Chain IDs:T (auth: K)
Chain Length:1297
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:O (auth: L)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:N
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:M (auth: O)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:K (auth: W)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:J (auth: X)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:H (auth: Y)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:B (auth: b)
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:E (auth: e)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Probable 18S rRNA (guanine-N(7))-methyltransferase
Gene (Uniprot):BUD23
Chain IDs:S (auth: q)
Chain Length:281
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Multifunctional methyltransferase subunit TRM112-like protein
Gene (Uniprot):TRMT112
Chain IDs:R (auth: r)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein TSR1 homolog
Gene (Uniprot):TSR1
Chain IDs:L (auth: u)
Chain Length:804
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein PNO1
Gene (Uniprot):PNO1
Chain IDs:I (auth: x)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein SLX9 homolog
Gene (Uniprot):SLX9
Chain IDs:U (auth: z)
Chain Length:230
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Nucleic Acids Res. 50 11924 11937 (2022)
PMID: 36321656 DOI: 10.1093/nar/gkac961

Abstact

Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.

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Primary Citation of related structures