5LZF

Structure of the 70S ribosome with fMetSec-tRNASec in the hybrid pre-translocation state (H)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

The pathway to GTPase activation of elongation factor SelB on the ribosome.

Fischer, N.Neumann, P.Bock, L.V.Maracci, C.Wang, Z.Paleskava, A.Konevega, A.L.Schroder, G.F.Grubmuller, H.Ficner, R.Rodnina, M.V.Stark, H.

(2016) Nature 540: 80-85

  • DOI: 10.1038/nature20560
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA Sec ) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA Sec recodes a UGA stop codon ne ...

    In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA Sec ) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA Sec recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA Sec binding by SelB and show large-scale rearrangements of Sec-tRNA Sec . Upon initial binding of SelB-Sec-tRNA Sec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA Sec covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA Sec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.


    Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
206Escherichia coliMutation(s): 0 
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
205Escherichia coliMutation(s): 0 
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
100Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
151Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
129Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
127Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
98Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
116Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
114Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
100Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
88Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
82Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
65Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
86Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
85Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
65Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
177Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
143Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
93Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
75Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
56Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
123Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
80Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
218Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
102Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
157Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
50Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
66Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1539Escherichia coli

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Entity ID: 23
MoleculeChainsLengthOrganism
SECIS mRNAx48Escherichia coli

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Entity ID: 24
MoleculeChainsLengthOrganism
fMetSec-tRNASecy95Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
23S ribosomal RNAA2903Escherichia coli

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Entity ID: 26
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli

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Entity ID: 22
MoleculeChainsLengthOrganism
tRNAfMetv77Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
4, 6
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanySonderforschungsbereich 860

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 2.0: 2019-02-20
    Changes: Data collection, Derived calculations, Polymer sequence