1HQ1

STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.

Batey, R.T.Sagar, M.B.Doudna, J.A.

(2001) J.Mol.Biol. 307: 229-246

  • DOI: 10.1006/jmbi.2000.4454

  • PubMed Abstract: 
  • The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core ...

    The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, P.O. Box 208114, New Haven, CT 06520-8814, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SIGNAL RECOGNITION PARTICLE PROTEIN
A
105Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ffh
Find proteins for P0AGD7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGD7
Entity ID: 1
MoleculeChainsLengthOrganism
4.5S RNA DOMAIN IVB49N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
B
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.555α = 90.00
b = 78.337β = 96.24
c = 32.872γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance