6TMF

Structure of an archaeal ABCE1-bound ribosomal post-splitting complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.

Nurenberg-Goloub, E.Kratzat, H.Heinemann, H.Heuer, A.Kotter, P.Berninghausen, O.Becker, T.Tampe, R.Beckmann, R.

(2020) EMBO J 39: e103788-e103788

  • DOI: https://doi.org/10.15252/embj.2019103788
  • Primary Citation of Related Structures:  
    6TMF

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt a.M., Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2195Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3193Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3Ae184Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4178Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4e241Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5220Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6e125Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7214Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8129Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8e126Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9132Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10102Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11133Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12144Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13136Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z56Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15151Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17111Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17e64Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19P115Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19e149Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein56Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S24e97Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S27e63Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S27ae50Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S28eAA [auth a]66Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeBA [auth b]123Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L41ECA [auth c]37Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ATPaseDA [auth d]594Saccharolobus solfataricusMutation(s): 2 
Gene Names: 
UniProt
Find proteins for Q980K5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,485Thermococcus celer Vu 13 = JCM 8558
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
LB [auth d],
NB [auth d]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
JB [auth d],
KB [auth d]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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FB [auth Q],
GB [auth W],
HB [auth W],
IB [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
EA [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EA [auth A],
EB [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
MB [auth d],
NA [auth A],
OA [auth A],
OB [auth d],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth A],
VA [auth A],
WA [auth A],
XA [auth A],
YA [auth A],
ZA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-05-13
    Changes: Database references