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PDBsum entry 2k0b

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protein links
Signaling protein PDB id
2k0b
Jmol
Contents
Protein chain
52 a.a. *
* Residue conservation analysis
PDB id:
2k0b
Name: Signaling protein
Title: Nmr structure of the uba domain of p62 (sqstm1)
Structure: Sequestosome-1. Chain: x. Fragment: uba domain (unp residues 387-436). Synonym: phosphotyrosine-independent ligand for the lck sh2 domain of 62 kda, ubiquitin-binding protein p62, ebi3- associated protein of 60 kda, p60, ebiap. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sqstm1, orca, osil. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 30 models
Authors: J.E.Long,B.Ciani,T.R.A.Gallagher,J.R.Cavey,P.W.Sheppard, R.Layfield,M.S.Searle
Key ref:
C.L.Evans et al. (2007). Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation. Proteins, 71, 227-240. PubMed id: 17932931 DOI: 10.1002/prot.21692
Date:
31-Jan-08     Release date:   19-Feb-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q13501  (SQSTM_HUMAN) -  Sequestosome-1
Seq:
Struc:
440 a.a.
52 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1002/prot.21692 Proteins 71:227-240 (2007)
PubMed id: 17932931  
 
 
Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation.
C.L.Evans, J.E.Long, T.R.Gallagher, J.D.Hirst, M.S.Searle.
 
  ABSTRACT  
 
The ubiquitin associated domain of p62 is a small three-helix bundle of approximately 50 residues that mediates the recognition of polyubiquitin chains and ubiquitylated substrates. The solution structure of a 52 residue construct containing this domain has been characterized using heteronuclear nuclear magnetic resonance (NMR) methods. The resulting ensemble of NMR-derived structures was used in molecular dynamics (MD) simulations to investigate the equilibrium conformation and dynamics of this domain. NOE and (15)N relaxation data have been used to validate the structural ensemble produced by the MD simulations and show a good correlation for residues in regions of secondary structure. A similar approach was taken using an ensemble of structures from the MD simulations to calculate electronic circular dichroism (CD) and IR spectra from first principles with an encouraging correlation with the experimental CD and IR data. Proteins 2007. (c) 2007 Wiley-Liss, Inc.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Histograms of properties calculated from the MD generated ensemble of structures. Filled black bars indicate the averages for each parameter calculated from the structures present in the first frames of the production dynamics. (a) Percentage of native contacts of the structures sampled during the MD simulations. (b) Percentage helical structure of the conformers. (c) distance between the second and third helix. (d) Percentage of NOE distance restraints violated. (e) Radius of gyration. (f) All-atom RMSD from the first conformer of the NMR ensemble.
Figure 6.
Figure 6. The relaxation parameters for the backbone ^15N nuclei in the p62-UBA domain, as found experimentally and the average calculated parameters from the series of simulations: black line with error bars, experimental data: grey line with error bars, calculated data. Error bars reflect one standard deviation. (a) Longitudinal (R[1]) relaxation rate. (b) Transverse (R[2]) relaxation rate. (c) Heteronuclear NOE values. (d) Generalized squared order parameters (S^2).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 71, 227-240) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18652480 K.Wong, J.A.Beckstead, D.Lee, P.M.Weers, E.Guigard, C.M.Kay, and R.O.Ryan (2008).
The N-terminus of apolipoprotein A-V adopts a helix bundle molecular architecture.
  Biochemistry, 47, 8768-8774.  
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