2HBA

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Energetically significant networks of coupled interactions within an unfolded protein.

Cho, J.H.Meng, W.Sato, S.Kim, E.Y.Schindelin, H.Raleigh, D.P.

(2014) Proc.Natl.Acad.Sci.USA 111: 12079-12084

  • DOI: 10.1073/pnas.1402054111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Unfolded and partially unfolded proteins participate in a wide range of biological processes from pathological aggregation to the regulation of normal cellular activity. Unfolded states can be populated under strongly denaturing conditions, but the e ...

    Unfolded and partially unfolded proteins participate in a wide range of biological processes from pathological aggregation to the regulation of normal cellular activity. Unfolded states can be populated under strongly denaturing conditions, but the ensemble which is relevant for folding, stability, and aggregation is that populated under physiological conditions. Characterization of nonnative states is critical for the understanding of these processes, yet comparatively little is known about their energetics and their structural propensities under native conditions. The standard view is that energetically significant coupled interactions involving multiple residues are generally not present in the denatured state ensemble (DSE) or in intrinsically disordered proteins. Using the N-terminal domain of the ribosomal protein L9, a small α-β protein, as an experimental model system, we demonstrate that networks of energetically significant, coupled interactions can form in the DSE of globular proteins, and can involve residues that are distant in sequence and spatially well separated in the native structure. X-ray crystallography, NMR, dynamics studies, native state pKa measurements, and thermodynamic analysis of more than 25 mutants demonstrate that residues are energetically coupled in the DSE. Altering these interactions by mutation affects the stability of the domain. Mutations that alter the energetics of the DSE can impact the analysis of cooperativity and folding, and may play a role in determining the propensity to aggregate.


    Organizational Affiliation

    Department of Biochemistry, Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794; and.,Rudolf Virchow Center for Experimental Biomedicine and Institute of Structural Biology, University of Würzburg, 97080 Würzburg, Germany.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794;,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794; daniel.raleigh@stonybrook.edu.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
A, B
52Geobacillus stearothermophilusMutation(s): 1 
Gene Names: rplI
Find proteins for P02417 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02417
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.614α = 90.00
b = 74.416β = 90.00
c = 50.755γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
ADSCdata collection
REFMACrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-08-13
    Type: Database references
  • Version 1.4: 2014-09-24
    Type: Database references
  • Version 1.5: 2017-10-18
    Type: Refinement description