6ZV6 image
Deposition Date 2020-07-24
Release Date 2021-05-12
Last Version Date 2025-04-09
Entry Detail
PDB ID:
6ZV6
Keywords:
Title:
Human RIO1(kd)-StHA late pre-40S particle, structural state B (post 18S rRNA cleavage)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:A (auth: 2)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:B (auth: A)
Chain Length:115
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:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:D (auth: C)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:E (auth: D)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:F (auth: E)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: F)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:H (auth: 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:I (auth: H)
Chain Length:568
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:J (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:K (auth: J)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:L (auth: K)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:M (auth: L)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:N (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:O (auth: 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:P (auth: O)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:Q (auth: P)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:R (auth: Q)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:S (auth: R)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:T (auth: S)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:HA (auth: T)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:V (auth: U)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:W (auth: V)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:X (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:Y (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:Z (auth: Y)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:AA (auth: Z)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:U (auth: a)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:BA (auth: b)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:CA (auth: c)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:DA (auth: d)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:EA (auth: e)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:FA (auth: f)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:GA (auth: g)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase RIO1
Gene (Uniprot):RIOK1
Chain IDs:IA (auth: h)
Chain Length:568
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PHD IA ASP modified residue
Primary Citation
The final step of 40S ribosomal subunit maturation is controlled by a dual key lock.
Elife 10 ? ? (2021)
PMID: 33908345 DOI: 10.7554/eLife.61254

Abstact

Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.

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Primary Citation of related structures