6ORL

RF1 pre-accommodated 70S complex at 24 ms


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

Fu, Z.Indrisiunaite, G.Kaledhonkar, S.Shah, B.Sun, M.Chen, B.Grassucci, R.A.Ehrenberg, M.Frank, J.

(2019) Nat Commun 10: 2579-2579

  • DOI: 10.1038/s41467-019-10608-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of ...

    When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. jf2192@cumc.columbia.edu.



Macromolecules

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
151Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 10
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: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
119Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
94Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
76Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
62Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
56Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
52Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
64Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coliMutation(s): 0 
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
225Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
208Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
205Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
156Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
k
104Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
129Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
127Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
271Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
99Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
117Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
123Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
116Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
100Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
88Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
80Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
66Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
83Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
86Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
70Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
FME-PHE-PHE
H
3Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
A
257Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
177Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
175Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
P-tRNA576Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganism
mRNA49Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
1, 2, 3, C, b, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
qL-PEPTIDE LINKINGC5 H9 N O4 SASP
FME
Query on FME
HL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM55440
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other