5LZB

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1038/nature20560
  • Primary Citation of Related Structures:  
    5LZA, 5LZB, 5LZC, 5LZD, 5LZE, 5LZF

  • 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 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]218Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]206Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]205Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]157Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]100Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]151Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]129Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]127Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]98Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]116Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]123Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]114Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth n]100Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]88Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]80Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]65Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]79Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]85Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth u]65Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Selenocysteine-specific elongation factorY [auth z]614Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth C]271Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth F]177Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth G]176Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11GA [auth I]141Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth K]122Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth L]143Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth M]136Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth N]120Escherichia coliMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L18NA [auth O]116Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth T]93Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth U]102Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth W]75Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth X]77Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29XA [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30YA [auth Z]58Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth 0]56Escherichia coliMutation(s): 0 
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UniProt GroupP0A7N4
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth 1]50Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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UniProt GroupP0A7N9
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth 2]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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UniProt GroupP0A7P5
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth 3]64Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DB [auth 4]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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UniProt GroupP0A7Q6
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EB [auth 6]66Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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UniProt GroupP0A7M9
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth a]1,539Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
fMet-tRNAfMetV [auth v]77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
SECIS mRNAW [auth x]48Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
Sec-tRNASecX [auth y]95Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAZ [auth A]2,903Escherichia coli
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNAAA [auth B]120Escherichia coli
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Entity ID: 58
MoleculeChains LengthOrganismImage
CCA 3' end of E-site tRNASec (low occupancy)FB [auth w]3Escherichia coli
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
IB [auth z]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FME
Query on FME

Download Ideal Coordinates CCD File 
GB [auth v]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
SEC
Query on SEC

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HB [auth y]SELENOCYSTEINE
C3 H7 N O2 Se
ZKZBPNGNEQAJSX-REOHCLBHSA-N
ZN
Query on ZN

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KB [auth 4],
LB [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
JB [auth z]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta3.5
MODEL REFINEMENTCoot0.8.3
MODEL REFINEMENTRCrane1.1
MODEL REFINEMENTPHENIX1.10.1 & developmental
MODEL REFINEMENTPHENIX1.10.1
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTERRASER

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanySonderforschungsbereich 860

Revision History  (Full details and data files)

  • 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, Structure summary
  • Version 2.1: 2024-04-24
    Changes: Data collection, Database references, Derived calculations