6ND4 image
Deposition Date 2018-12-13
Release Date 2019-06-19
Last Version Date 2024-03-20
Entry Detail
PDB ID:
6ND4
Keywords:
Title:
Conformational switches control early maturation of the eukaryotic small ribosomal subunit
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
4.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5'ETS rRNA
Chain IDs:A (auth: 0)
Chain Length:700
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:18S rRNA 5' domain start
Chain IDs:B (auth: 1)
Chain Length:15
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:C (auth: 2)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Mpp10
Gene (Uniprot):MPP10
Chain IDs:T (auth: A)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Bud21
Gene (Uniprot):BUD21
Chain IDs:U (auth: D)
Chain Length:327
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp17
Chain IDs:D (auth: H)
Chain Length:853
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp8
Chain IDs:E (auth: I)
Chain Length:519
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp15
Gene (Uniprot):UTP15
Chain IDs:F (auth: J)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp9
Chain IDs:G (auth: K)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp5
Gene (Uniprot):UTP5
Chain IDs:H (auth: L)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp10
Gene (Uniprot):UTP10
Chain IDs:I (auth: M)
Chain Length:1769
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp4
Chain IDs:J (auth: N)
Chain Length:727
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp1
Gene (Uniprot):PWP2
Chain IDs:K (auth: O)
Chain Length:923
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp6
Chain IDs:L (auth: P)
Chain Length:421
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp12
Chain IDs:M (auth: Q)
Chain Length:917
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp13
Chain IDs:N (auth: R)
Chain Length:736
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp18
Gene (Uniprot):UTP18
Chain IDs:O (auth: S)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp21
Gene (Uniprot):UTP21
Chain IDs:P (auth: T)
Chain Length:939
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Sof1
Gene (Uniprot):SOF1
Chain IDs:Q (auth: U)
Chain Length:489
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp7
Gene (Uniprot):UTP7
Chain IDs:R (auth: W)
Chain Length:554
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Imp3
Gene (Uniprot):IMP3
Chain IDs:S (auth: Z)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nop56
Chain IDs:V (auth: a)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nop58
Chain IDs:W (auth: b)
Chain Length:503
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nop1.1
Gene (Uniprot):NOP1
Chain IDs:X (auth: c), Y (auth: d)
Chain Length:327
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Snu13
Gene (Uniprot):SNU13
Chain IDs:Z (auth: e), AA (auth: f)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Rrp9
Gene (Uniprot):RRP9
Chain IDs:BA (auth: g)
Chain Length:573
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Utp24
Gene (Uniprot):FCF1
Chain IDs:CA (auth: l)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Unidentified fragment
Chain IDs:DA (auth: x)
Chain Length:24
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Ligand Molecules
Primary Citation
Conformational switches control early maturation of the eukaryotic small ribosomal subunit.
Elife 8 ? ? (2019)
PMID: 31206356 DOI: 10.7554/eLife.45185

Abstact

Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5' external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5' external transcribed spacer ribonucleoprotein - provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly.

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Primary Citation of related structures