1HC8

CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Compact RNA Tertiary Structure Contains a Buried Backbone-K+ Complex

Conn, G.L.Gittis, A.G.Lattman, E.E.Misra, V.K.Draper, D.E.

(2002) J.Mol.Biol. 318: 963

  • DOI: 10.1016/S0022-2836(02)00147-X

  • PubMed Abstract: 
  • The structure of a 58 nucleotide ribosomal RNA fragment buries several phosphate groups of a hairpin loop within a large tertiary core. During refinement of an X-ray crystal structure containing this RNA, a potassium ion was found to be contacted by ...

    The structure of a 58 nucleotide ribosomal RNA fragment buries several phosphate groups of a hairpin loop within a large tertiary core. During refinement of an X-ray crystal structure containing this RNA, a potassium ion was found to be contacted by six oxygen atoms from the buried phosphate groups; the ion is contained completely within the solvent-accessible surface of the RNA. The electrostatic potential at the ion chelation site is unusually large, and more than compensates for the substantial energetic penalties associated with partial dehydration of the ion and displacement of delocalized ions. The very large predicted binding free energy, approximately -30 kcal/mol, implies that the site must be occupied for the RNA to fold. These findings agree with previous studies of the ion-dependent folding of tertiary structure in this RNA, which concluded that a monovalent ion was bound in a partially dehydrated environment where Mg2+ could not easily compete for binding. By compensating the unfavorable free energy of buried phosphate groups with a chelated ion, the RNA is able to create a larger and more complex tertiary fold than would be possible otherwise.


    Related Citations: 
    • Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
      Conn, G.L.,Draper, D.E.,Lattman, E.E.,Gittis, A.G.
      (1999) Science 284: 1171


    Organizational Affiliation

    Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L11
A, B
76Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rplK
Find proteins for P56210 (Geobacillus stearothermophilus)
Go to UniProtKB:  P56210
Entity ID: 2
MoleculeChainsLengthOrganism
58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAINC,D58Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OS
Query on OS

Download SDF File 
Download CCD File 
C, D
OSMIUM ION
Os
XQBKHDFIPARBOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
C, D
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 150.675α = 90.00
b = 150.675β = 90.00
c = 63.841γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance