5LZB

Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the initial binding state (IB)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 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 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
  • Primary Citation of Related Structures:  5LZA, 5LZC, 5LZD, 5LZE, 5LZF

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

    In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNASec) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNASec 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-tRNASec binding by SelB and show large-scale rearrangements of Sec-tRNASec. Upon initial binding of SelB-Sec-tRNASec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNASec 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-tRNASec 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S2
b
218 Escherichia coli (strain K12) Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S3
c
206 Escherichia coli (strain K12) Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S4
d
205 Escherichia coli (strain K12) Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S5
e
157 Escherichia coli (strain K12) Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 6
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S6
f
100 Escherichia coli (strain K12) Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S7
g
151 Escherichia coli (strain K12) Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S8
h
129 Escherichia coli (strain K12) Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S9
i
127 Escherichia coli (strain K12) Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S10
j
98 Escherichia coli (strain K12) Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 11
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S11
k
116 Escherichia coli (strain K12) Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S12
l
123 Escherichia coli (strain K12) Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 13
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S13
m
114 Escherichia coli (strain K12) Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S14
n
100 Escherichia coli (strain K12) Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S15
o
88 Escherichia coli (strain K12) Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 16
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S16
p
82 Escherichia coli (strain K12) Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 17
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S17
q
80 Escherichia coli (strain K12) Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 18
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S18
r
65 Escherichia coli (strain K12) Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S19
s
79 Escherichia coli (strain K12) Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S20
t
85 Escherichia coli (strain K12) Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
Molecule Chains Sequence Length Organism Details
30S ribosomal protein S21
u
65 Escherichia coli (strain K12) Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 25
Molecule Chains Sequence Length Organism Details
Selenocysteine-specific elongation factor
z
614 Escherichia coli (strain K12) Gene Names: selB (fdhA)
Find proteins for P14081 (Escherichia coli (strain K12))
Go to UniProtKB:  P14081
Entity ID: 28
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L2
C
271 Escherichia coli (strain K12) Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 29
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L3
D
209 Escherichia coli (strain K12) Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 30
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L4
E
201 Escherichia coli (strain K12) Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 31
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L5
F
177 Escherichia coli (strain K12) Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 32
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L6
G
176 Escherichia coli (strain K12) Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 33
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L11
I
141 Escherichia coli (strain K12) Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 34
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L9
H
149 Escherichia coli (strain K12) Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 35
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L13
J
142 Escherichia coli (strain K12) Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 36
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L14
K
122 Escherichia coli (strain K12) Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 37
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L15
L
143 Escherichia coli (strain K12) Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 38
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L16
M
136 Escherichia coli (strain K12) Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 39
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L17
N
120 Escherichia coli (strain K12) Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 40
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L18
O
116 Escherichia coli (strain K12) Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 41
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L19
P
114 Escherichia coli (strain K12) Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 42
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L20
Q
117 Escherichia coli (strain K12) Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 43
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L21
R
103 Escherichia coli (strain K12) Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 44
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L22
S
110 Escherichia coli (strain K12) Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 45
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L23
T
93 Escherichia coli (strain K12) Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 46
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L24
U
102 Escherichia coli (strain K12) Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 47
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L25
V
94 Escherichia coli (strain K12) Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 48
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L27
W
75 Escherichia coli (strain K12) Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 49
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L28
X
77 Escherichia coli (strain K12) Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 50
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L29
Y
63 Escherichia coli (strain K12) Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 51
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L30
Z
58 Escherichia coli (strain K12) Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 52
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L32
0
56 Escherichia coli (strain K12) Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 53
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L33
1
50 Escherichia coli (strain K12) Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 54
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L34
2
46 Escherichia coli (strain K12) Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 55
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L35
3
64 Escherichia coli (strain K12) Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 56
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L36
4
38 Escherichia coli (strain K12) Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 57
Molecule Chains Sequence Length Organism Details
50S ribosomal protein L31
6
66 Escherichia coli (strain K12) Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 1
Molecule Chains Length Organism
16S ribosomal RNA a 1539 Escherichia coli
Entity ID: 22
Molecule Chains Length Organism
fMet-tRNAfMet v 77 Escherichia coli
Entity ID: 23
Molecule Chains Length Organism
SECIS mRNA x 48 Escherichia coli
Entity ID: 24
Molecule Chains Length Organism
Sec-tRNASec y 95 Escherichia coli
Entity ID: 26
Molecule Chains Length Organism
23S ribosomal RNA A 2903 Escherichia coli
Entity ID: 27
Molecule Chains Length Organism
5S ribosomal RNA B 120 Escherichia coli
Entity ID: 58
Molecule Chains Length Organism
CCA 3' end of E-site tRNASec (low occupancy) w 3 Escherichia coli
Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

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Download CCD File 
4, 6
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SEC
Query on SEC

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Download CCD File 
y
SELENOCYSTEINE
C3 H7 N O2 Se
ZKZBPNGNEQAJSX-REOHCLBHSA-N
 Ligand Interaction
FME
Query on FME

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Download CCD File 
v
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
z
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  18 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
a, A, v, y
RNA LINKING C9 H13 N2 O9 P U
5MC
Query on 5MC
A, a
RNA LINKING C10 H16 N3 O8 P C
6MZ
Query on 6MZ
A
RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
A
RNA LINKING C10 H15 N2 O9 P U
1MG
Query on 1MG
A
RNA LINKING C11 H16 N5 O8 P G
OMC
Query on OMC
A
RNA LINKING C10 H16 N3 O8 P C
MA6
Query on MA6
a
RNA LINKING C12 H18 N5 O7 P A
4SU
Query on 4SU
v
RNA LINKING C9 H13 N2 O8 P S U
2MG
Query on 2MG
A, a
RNA LINKING C11 H16 N5 O8 P G
G7M
Query on G7M
A, a
RNA LINKING C11 H17 N5 O8 P G
UR3
Query on UR3
a
RNA LINKING C10 H15 N2 O9 P U
OMG
Query on OMG
A
RNA LINKING C11 H16 N5 O8 P G
6IA
Query on 6IA
y
RNA LINKING C15 H24 N5 O7 P A
5MU
Query on 5MU
A, v, y
RNA LINKING C10 H15 N2 O9 P U
2MA
Query on 2MA
A
RNA LINKING C11 H16 N5 O7 P A
4OC
Query on 4OC
a
RNA LINKING C11 H18 N3 O8 P C
3TD
Query on 3TD
A
RNA LINKING C10 H15 N2 O9 P U
H2U
Query on H2U
A, v, y
RNA LINKING C9 H15 N2 O9 P U
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding Organization Country Grant Number
German Research Foundation Germany FOR1805
German Research Foundation Germany Sonderforschungsbereich 860

Revision History 

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