1ML5

Structure of the E. coli ribosomal termination complex with release factor 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Escherichia coli ribosomal termination complex with release factor 2

Klaholz, B.P.Pape, T.Zavialov, A.V.Myasnikov, A.G.Orlova, E.V.Vestergaard, B.Ehrenberg, M.van Heel, M.

(2003) Nature 421: 90-94

  • DOI: 10.1038/nature01225
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of ...

    Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.


    Organizational Affiliation

    Department of Biological Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AY, UK.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
H
162Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
I
101Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
J
156Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
K
138Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
L
128Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
M
105Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
N
129Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
O
135Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
P
126Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
Q
61Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
R
89Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
S
91Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
T
105Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
U
88Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
V
93Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
W
106Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
X
26Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L1
c
228Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
d
178Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
e
338Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
f
246Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
g
176Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
h
177Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
l
141Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
m
145Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
n
122Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
o
164Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
p
138Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
q
186Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
r
66Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
s
113Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
t
84Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
u
119Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
v
94Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
w
70Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
x
60Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
Z
365Escherichia coliMutation(s): 0 
Gene Names: prfB/SupK
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
E
256Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
F
239Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
G
209Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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MoleculeChainsLengthOrganism
30S 16S RIBOSOMAL RNAA1522Escherichia coli

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T-RNA(PHE)B76Escherichia coli
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A- AND P-SITE MESSENGER RNA CODONSC6Escherichia coli

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-12-18
    Changes: Advisory, Derived calculations, Other