6TMF image
Deposition Date 2019-12-04
Release Date 2020-02-12
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6TMF
Keywords:
Title:
Structure of an archaeal ABCE1-bound ribosomal post-splitting complex
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:66
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rps2
Chain IDs:B
Chain Length:195
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rps3
Chain IDs:C
Chain Length:193
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3Ae
Gene (Uniprot):rps3ae
Chain IDs:D
Chain Length:594
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rps4
Chain IDs:E
Chain Length:178
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4e
Gene (Uniprot):rps4e
Chain IDs:F
Chain Length:241
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rps5
Chain IDs:G
Chain Length:220
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6e
Gene (Uniprot):rps6e
Chain IDs:H
Chain Length:125
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rps7
Chain IDs:I
Chain Length:214
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rps8
Chain IDs:J
Chain Length:129
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8e
Gene (Uniprot):rps8e
Chain IDs:K
Chain Length:126
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rps9
Chain IDs:L
Chain Length:132
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rps10p
Chain IDs:M
Chain Length:102
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rps11
Chain IDs:N
Chain Length:133
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rps12
Chain IDs:O
Chain Length:144
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rps13
Chain IDs:P
Chain Length:136
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rps14P
Chain IDs:Q
Chain Length:56
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rps15
Chain IDs:R
Chain Length:151
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rps17
Chain IDs:S
Chain Length:111
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17e
Gene (Uniprot):rps17e
Chain IDs:T
Chain Length:64
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19P
Gene (Uniprot):rps19p
Chain IDs:U
Chain Length:115
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19e
Gene (Uniprot):rps19e
Chain IDs:V
Chain Length:149
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein
Gene (Uniprot):A3L02_01275
Chain IDs:W
Chain Length:56
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S24e
Gene (Uniprot):rps24e
Chain IDs:X
Chain Length:97
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S27e
Gene (Uniprot):rps27e
Chain IDs:Y
Chain Length:63
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S27ae
Gene (Uniprot):rps27ae
Chain IDs:Z
Chain Length:50
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S28e
Gene (Uniprot):rps28e
Chain IDs:AA (auth: a)
Chain Length:66
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7Ae
Gene (Uniprot):rpl7ae
Chain IDs:BA (auth: b)
Chain Length:195
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L41E
Gene (Uniprot):A3L02_06520
Chain IDs:CA (auth: c)
Chain Length:193
Number of Molecules:1
Biological Source:Thermococcus celer Vu 13 = JCM 8558
Polymer Type:polypeptide(L)
Molecule:ATPase
Mutations:E238A, E485A
Chain IDs:DA (auth: d)
Chain Length:594
Number of Molecules:1
Biological Source:Saccharolobus solfataricus
Primary Citation
Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.
Embo J. 39 e103788 e103788 (2020)
PMID: 32064661 DOI: 10.15252/embj.2019103788

Abstact

Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we captured the archaeal 30S ribosome post-splitting complex at 2.8 Å resolution by cryo-electron microscopy. The structure reveals the dynamic behavior of structural motifs unique to ABCE1, which ultimately leads to ribosome splitting. More specifically, we provide molecular details on how conformational rearrangements of the iron-sulfur cluster domain and hinge regions of ABCE1 are linked to closure of its nucleotide-binding sites. The combination of mutational and functional analyses uncovers an intricate allosteric network between the ribosome, regulatory domains of ABCE1, and its two structurally and functionally asymmetric ATP-binding sites. Based on these data, we propose a refined model of how signals from the ribosome are integrated into the ATPase cycle of ABCE1 to orchestrate ribosome recycling.

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