Macromolecule Content

• Total Structure Weight: 17153.66 
• Atom Count: 1148 
• Residue Count: 152 
• Unique protein chains: 1

2PE9

NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements

• DOI: 10.2210/pdb2PE9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2007-04-02 Released: 2007-07-10 
• Deposition Author(s): Ryabov, Y., Fushman, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

Ryabov, Y., Fushman, D.

(2007) J.Am.Chem.Soc. 129: 7894-7902

• PubMed: 17550252 
• DOI: 10.1021/ja071185d
• Primary Citation of Related Structures:  
  2PEA


• PubMed Abstract: 
  

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

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Related Citations: 

• Structural Properties of Polyubiquitin Chains in Solution
  Varadan, R.,Walker, O.,Picart, C.,Fushman, D.
  (2002) J.Mol.Biol. 324: 637
• An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation.
  Ryabov, Y.,Geraghty, C.,Varshney, A.,Fushman, D.
  (2006) J.Am.Chem.Soc. 128: 15432
• A Model of Interdomain Mobility in a Multidomain Protein
  Ryabov, Y.,Fushman, D.
  (2007) J.Am.Chem.Soc. 129: 3315




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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	A, B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-02 
• Released Date: 2007-07-10 
• Deposition Author(s): Ryabov, Y., Fushman, D.

Revision History 

• Version 1.0: 2007-07-10
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance