1ML5

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14 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 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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
Z
365Escherichia coli (strain K12)Gene Names: prfB (supK)
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
E
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
F
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
G
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
H
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
I
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
J
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
K
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
L
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
M
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
N
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
O
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
P
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
Q
61Thermus aquaticusGene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
R
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
S
91Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
T
105Thermus aquaticusGene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
U
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
V
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
W
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
X
26Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L1
c
228Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
d
178Geobacillus stearothermophilusGene Names: rplB
Find proteins for P04257 (Geobacillus stearothermophilus)
Go to UniProtKB:  P04257
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
e
338Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl3
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
f
246Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl4
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
g
176Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl5
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
h
177Geobacillus kaustophilus (strain HTA426)Gene Names: rplF
Find proteins for Q5L408 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L408
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
l
141Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
m
145Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl13
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
n
122Geobacillus kaustophilus (strain HTA426)Gene Names: rplN
Find proteins for Q5L413 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L413
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
o
164Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl15
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
p
138Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl10e
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60617
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
q
186Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl18
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
r
66Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl24e
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
s
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
t
84Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl23p
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
u
119Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl24p
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
v
94Escherichia coli (strain K12)Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
w
70Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl29p
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
x
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 1
MoleculeChainsLengthOrganism
30S 16S RIBOSOMAL RNAA1522Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
T-RNA(PHE)B76Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
A- AND P-SITE MESSENGER RNA CODONSC6Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
50S 23S RIBOSOMAL RNAa2916Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
50S 5S RIBOSOMAL RNAb123Escherichia coli
Small Molecules
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
B
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
B
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
B
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
B
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
B
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
B
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
B
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
B
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
B
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
B
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14 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: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance