6OGG

70S termination complex with RF2 bound to the UGA codon. Rotated ribosome with RF2 bound (Structure IV).

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Extensive ribosome and RF2 rearrangements during translation termination.

Svidritskiy, E., Demo, G., Loveland, A.B., Xu, C., Korostelev, A.A.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.46850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, ...

    Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.

    Organizational Affiliation: 

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
b
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
c
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
d
201Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplD
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
e
179Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplE
Find proteins for D7Z9G7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
f
177Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplF
Find proteins for D7Z9H0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
g
149Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplI
Find proteins for D7ZI15 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI15
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
j
142Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplM
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZET0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
k
123Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplN
Find proteins for D7Z9G5 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
l
144Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for A0A037Y8L6 (Escherichia coli)
Go to UniProtKB:  A0A037Y8L6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
m
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
n
127Escherichia coli O81 (strain ED1a)Mutation(s): 0 
Gene Names: rplQ
Find proteins for B7N179 (Escherichia coli O81 (strain ED1a))
Go to UniProtKB:  B7N179
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
o
117Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplR
Find proteins for D7Z9H1 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
p
115Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplS
Find proteins for D7ZKU3 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZKU3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
q
118Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplT
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
r
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplU
Find proteins for D7ZEN7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEN7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
s
110Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7Z9G0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
t
100Escherichia coli MS 198-1Mutation(s): 0 
Gene Names: rplW
Find proteins for D7X2Z9 (Escherichia coli MS 198-1)
Go to UniProtKB:  D7X2Z9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
u
104Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplX
Find proteins for D7Z9G6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
v
94Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rplY
Find proteins for D7XH79 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XH79
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
w
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
x
78Escherichia coli KTE38Mutation(s): 0 
Gene Names: rpmB
Find proteins for S0YB49 (Escherichia coli KTE38)
Go to UniProtKB:  S0YB49
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
y
63Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmC
Find proteins for D7Z9G3 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G3
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
z
59Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmD
Find proteins for D7Z9H3 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B
57Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmF
Find proteins for D7ZGG2 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZGG2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
C
55Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmG
Find proteins for D7Z9P0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9P0
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
D
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
E
65Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpmI
Find proteins for D7Z814 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z814
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
F
38Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L017
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
G
241Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsB
Find proteins for D7ZK99 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZK99
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
H
233Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsC
Find proteins for B7MCS9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
I
206Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsD
Find proteins for D7Z9H7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
J
167Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsE
Find proteins for D7Z9H2 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
K
131Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsF
Find proteins for D7ZI17 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI17
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
L
156Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsG
Find proteins for D7ZAN1 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZAN1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
M
130Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsH
Find proteins for D7Z9G9 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G9
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
N
130Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsI
Find proteins for D7ZES9 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZES9
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
O
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsJ
Find proteins for D7Z9F4 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F4
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
P
129Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsK
Find proteins for B7MCR3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
Q
124Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsL
Find proteins for D7ZAN0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZAN0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
R
118Escherichia coli DEC6AMutation(s): 0 
Gene Names: rpsM
Find proteins for H4UQ02 (Escherichia coli DEC6A)
Go to UniProtKB:  H4UQ02
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
S
101Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsN
Find proteins for D7Z9G8 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
T
89Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsO
Find proteins for D7ZEL4 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEL4
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
U
82Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
V
84Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsQ
Find proteins for D7Z9G4 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G4
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
W
75Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpsR
Find proteins for A0A0E2KXL3 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2KXL3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
X
92Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsS
Find proteins for D7Z9F9 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
Y
87Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsT
Find proteins for D7ZAS2 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZAS2
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
Z
71Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpsU
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L2J1
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
a
234Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplA
Find proteins for B7MIX0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX0
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
8
371Escherichia coliMutation(s): 0 
Gene Names: prfB
Find proteins for A0A2S5ZJX2 (Escherichia coli)
Go to UniProtKB:  A0A2S5ZJX2
Entity ID: 50
MoleculeChainsLengthOrganism
16S ribosomal RNA31539Escherichia coli
Entity ID: 51
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli
Entity ID: 52
MoleculeChainsLengthOrganism
5S ribosomal RNA2120Escherichia coli
Entity ID: 53
MoleculeChainsLengthOrganism
tRNAfMet577Escherichia coli
Entity ID: 54
MoleculeChainsLengthOrganism
mRNA427synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM107465
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127094

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release