2PLY | pdb_00002ply

Structure of the mRNA binding fragment of elongation factor SelB in complex with SECIS RNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.287 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB.

Soler, N.Fourmy, D.Yoshizawa, S.

(2007) J Mol Biology 370: 728-741

  • DOI: https://doi.org/10.1016/j.jmb.2007.05.001
  • Primary Citation Related Structures: 
    2PJP, 2PLY

  • PubMed Abstract: 

    Elongation factor SelB is responsible for co-translational incorporation of selenocysteine (Sec) into proteins. The UGA stop codon is recoded as a Sec codon in the presence of a downstream mRNA hairpin. In prokaryotes, in addition to the EF-Tu-like N-terminal domains, a C-terminal extension containing four tandem winged-helix motifs (WH1-4) recognizes the mRNA hairpin. The 2.3-A resolution crystal structure of the Escherichia coli WH3/4 domains bound to mRNA with mutagenesis data reveal that the two WH motifs use the same structural elements to bind RNA. The structure together with the 2.6-A resolution structure of the WH1-4 domains from Moorella thermoacetica bound to RNA revealed that a salt bridge connecting WH2 to WH3 modules is disrupted upon mRNA binding. The results provide a structural basis for the molecular switch that may allow communication between tRNA and mRNA binding sites and illustrate how RNA acts as an activator of the switch. The structures show that tandem WH motifs not only provide an excellent scaffold for RNA binding but can also have an active role in the function of protein-RNA complexes.


  • Organizational Affiliation
    • Laboratoire de Chimie et Biologie Structurales, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France.

Macromolecule Content 

  • Total Structure Weight: 74.91 kDa 
  • Atom Count: 4,422 
  • Modeled Residue Count: 456 
  • Deposited Residue Count: 562 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Selenocysteine-specific elongation factorC [auth A],
D [auth B]
258Neomoorella thermoaceticaMutation(s): 2 
Gene Names: selB
UniProt
Find proteins for Q46455 (Neomoorella thermoacetica)
Explore Q46455 
Go to UniProtKB:  Q46455
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46455
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3')A [auth C],
B [auth E]
23N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
U [auth A],
V [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth B],
W [auth A],
X [auth A],
Y [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth B]
E [auth C]
F [auth C]
G [auth C]
H [auth C]
AA [auth B],
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth E],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.287 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.64α = 90
b = 120.838β = 100.18
c = 50.865γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Xnemodata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description