2RDO

50S subunit with EF-G(GDPNP) and RRF bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 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

Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.

Gao, N.Zavialov, A.V.Ehrenberg, M.Frank, J.

(2007) J Mol Biol 374: 1345-1358

  • DOI: 10.1016/j.jmb.2007.10.021
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Ba ...

    After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF-containing posttermination ribosome triggers an interdomain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9-A (Fourier shell correlation cutoff of 0.5) cryo-electron microscopy map of a 50S x EF-G x guanosine 5'-[(betagamma)-imido]triphosphate x RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the noncleavable GTP analogue guanosine 5'-[(betagamma)-imido]triphosphate. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in transfer RNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G's domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits.


    Related Citations: 
    • Structural insights into fusidic acid resistance and sensitivity in EF-G.
      Hansson, S., Singh, R., Gudkov, A.T., Liljas, A., Logan, D.T.
      (2005) J Mol Biol 348: 939
    • Structures of the bacterial ribosome at 3.5 A resolution.
      Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H.
      (2005) Science 310: 827
    • Crystal structure of the ribosome recycling factor from Escherichia coli.
      Kim, K.K., Min, K., Suh, S.W.
      (2000) EMBO J 19: 2362
    • Structure of the L1 protuberance in the ribosome.
      Nikulin, A., Eliseikina, I., Tishchenko, S., Nevskaya, N., Davydova, N., Platonova, O., Piendl, W., Selmer, M., Liljas, A., Drygin, D., Zimmermann, R., Garber, M., Nikonov, S.
      (2003) Nat Struct Mol Biol 10: 104
    • Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
      Gao, N., Zavialov, A.V., Li, W., Sengupta, J., Valle, M., Gursky, R.P., Ehrenberg, M., Frank, J.
      (2005) Mol Cell 18: 663

    Organizational Affiliation

    Howard Hughes Medical Institute, Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
272Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
178Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
84Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
X
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Y
58Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
Z
70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
54Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
9
233Escherichia coliMutation(s): 0 
Find proteins for P0A7L0 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Elongation factor G
7
704Escherichia coliMutation(s): 0 
Find proteins for P0A6M8 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosome recycling factor
8
185Escherichia coliMutation(s): 0 
Find proteins for P0A805 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A805

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Entity ID: 1
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAA120Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAB2904Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Data collection