3LQX

SRP ribonucleoprotein core complexed with cobalt hexammine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and Energetic Analysis of Metal Ions Essential to SRP Signal Recognition Domain Assembly

Batey, R.T.Doudna, J.A.

(2002) Biochemistry 41: 11703-11710

  • DOI: https://doi.org/10.1021/bi026163c
  • Primary Citation of Related Structures:  
    3LQX

  • PubMed Abstract: 

    The signal recognition particle (SRP) targets proteins to the endoplasmic reticulum in eukaryotes or to the inner membrane in prokaryotes by binding to hydrophobic signal sequences. Signal peptide recognition occurs within the highly conserved RNA-protein core of the SRP, underscoring the importance of this complex in SRP function. Structural analysis of the RNA and protein components of the prokaryotic SRP in the free and bound states revealed that the RNA undergoes a significant conformational change upon protein binding involving the uptake of several monovalent and divalent cations. To investigate the role of these metal ions in formation of the functional SRP complex, we used binding affinity assays and X-ray crystallography to analyze the specificity and energetic contributions of mono- and divalent metal ions bound in the RNA. Our results demonstrate that several metal ion binding sites important for RNA conformation can accommodate chemically distinct ions, often without affecting the structure of the complex. Thus, while these metal ions are highly ordered and essential for the formation and stability of the SRP complex, they behave like nonspecific metal ions.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle protein105Escherichia coliMutation(s): 1 
UniProt
Find proteins for P0AGD7 (Escherichia coli (strain K12))
Explore P0AGD7 
Go to UniProtKB:  P0AGD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGD7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
SRP RNA49N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
J [auth B]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.818α = 90
b = 77.765β = 94.08
c = 32.735γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-03-02 
  • Deposition Author(s): Batey, R.T.

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-01-21
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection