5LL6

Structure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.

Heuer, A.Gerovac, M.Schmidt, C.Trowitzsch, S.Preis, A.Kotter, P.Berninghausen, O.Becker, T.Beckmann, R.Tampe, R.

(2017) Nat. Struct. Mol. Biol. 24: 453-460

  • DOI: 10.1038/nsmb.3396

  • PubMed Abstract: 
  • The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we ...

    The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1. Notably, the movement implies a collision with A-site factors, thus explaining the splitting mechanism. Disruption of key interactions in the post-splitting complex impairs cellular homeostasis. Additionally, the structure of a native post-splitting complex reveals ABCE1 to be part of the 43S initiation complex, suggesting a coordination of termination, recycling, and initiation.


    Organizational Affiliation

    Gene Center and Center of Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
P
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
Q
255Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33442
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
R
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2
Go to UniProtKB:  P25443
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
T
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
U
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
V
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
W
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
X
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Y
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS13
Go to UniProtKB:  P05756
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
Z
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
a
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0V8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
b
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
c
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
d
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-A
e
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS26A (RPS26)
Find proteins for P39938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39938
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
f
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A
Go to UniProtKB:  P35997
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
g
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor RLI1
h
608Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RLI1
Find proteins for Q03195 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03195
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA21798Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
h
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
h
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
h
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Data collection