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 

wwPDB Validation 3D Report Full Report


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: 10.15252/embj.2019103788
  • Structures With Same Primary Citation

  • 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 ...

    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

    Department of Biochemistry, Gene Center, Ludwig-Maximilians University Munich, München, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
195Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps2A3L02_00670
Find proteins for A0A218NZR2 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZR2

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3Ae
D
184Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps3aeA3L02_02445
Find proteins for A0A218P0R0 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P0R0

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4e
F
241Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps4eA3L02_00835
Find proteins for A0A218NZX1 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZX1

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
G
220Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps5A3L02_00795
Find proteins for A0A218P4N5 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4N5

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
I
214Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps7A3L02_09870
Find proteins for A0A218P4K4 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4K4

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
J
129Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps8A3L02_00820
Find proteins for A0A218NZT7 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZT7

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
L
132Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps9A3L02_00695
Find proteins for A0A218NZS6 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZS6

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
M
102Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps10prps10A3L02_08320
Find proteins for A0A218P3Q8 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P3Q8

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
N
133Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps11A3L02_00720
Find proteins for A0A218NZU0 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZU0

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
P
136Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps13A3L02_00730
Find proteins for A0A218NZT2 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZT2

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
Q
56Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps14Prps14A3L02_00825
Find proteins for A0A218NZW1 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZW1

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
S
111Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps17A3L02_00850
Find proteins for A0A218NZX3 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZX3

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19e
V
149Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps19eA3L02_08625
Find proteins for A0A218P4W7 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4W7

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24e
X
97Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps24eA3L02_01605
Find proteins for A0A218P0B9 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P0B9

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27e
Y
63Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps27eA3L02_00590
Find proteins for A0A218NZS1 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZS1

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27ae
Z
50Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps27aeA3L02_01600
Find proteins for A0A218P0A5 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P0A5

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28e
a
66Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps28eA3L02_03310
Find proteins for A0A218P147 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P147

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L41E
c
37Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: A3L02_06520
Find proteins for A0A218P2S9 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P2S9

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ATPase
d
594Saccharolobus solfataricusMutation(s): 2 
Gene Names: 
Find proteins for A0A0E3MFT8 (Saccharolobus solfataricus)
Go to UniProtKB:  A0A0E3MFT8

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8e
K
126Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps8eA3L02_09610
Find proteins for A0A218P4F6 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4F6

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
O
144Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps12A3L02_09875
Find proteins for A0A218P4I2 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4I2

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
R
151Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps15A3L02_02460
Find proteins for A0A218P0Q1 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P0Q1

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17e
T
64Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps17eA3L02_05615
Find proteins for A0A218P2C1 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P2C1

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19P
U
115Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps19pA3L02_00880
Find proteins for A0A218P4M9 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P4M9

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein
W
56Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: A3L02_01275
Find proteins for A0A218P055 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P055

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
b
123Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rpl7aeA3L02_03315
Find proteins for A0A218P167 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P167

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
193Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps3A3L02_00870
Find proteins for A0A218NZU7 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZU7

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
E
178Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps4A3L02_00725
Find proteins for A0A218NZV3 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218NZV3

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6e
H
125Thermococcus celer Vu 13 = JCM 8558Mutation(s): 0 
Gene Names: rps6eA3L02_06645
Find proteins for A0A218P2W6 (Thermococcus celer Vu 13 = JCM 8558)
Go to UniProtKB:  A0A218P2W6

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1485Thermococcus celer Vu 13 = JCM 8558
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
d
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

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d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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Q, W, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, d
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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