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 
  • R-Value Observed: 0.145 

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 U S A 111: 12079-12084

  • DOI: 10.1073/pnas.1402054111
  • Primary Citation of Related Structures:  
    2HBB, 2HBA

  • 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 ensemble which is relevant for folding, stability, and aggregation is that populated under physiological conditions ...

    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 Chemistry, Stony Brook University, Stony Brook, NY 11794; daniel.raleigh@stonybrook.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9A, B52Geobacillus stearothermophilusMutation(s): 1 
Gene Names: rplI
Find proteins for P02417 (Geobacillus stearothermophilus)
Explore P02417 
Go to UniProtKB:  P02417
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
U [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , O [auth B] , P [auth B] , Q [auth B] , R [auth B] , 
F [auth A],  G [auth A],  H [auth A],  I [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • R-Value Observed: 0.145 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.614α = 90
b = 74.416β = 90
c = 50.755γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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