Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.58 kDa 
• Atom Count: 602 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

2NR2

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins

• PDB DOI: 10.2210/pdb2NR2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-01 Released: 2007-05-08 
• Deposition Author(s): Richter, B., Gsponer, J., Varnai, P., Salvatella, X., Vendruscolo, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 144 
• Conformers Submitted: 144 
• Selection Criteria: all calculated structures submitted 

Literature

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins

Richter, B., Gsponer, J., Varnai, P., Salvatella, X., Vendruscolo, M.

(2007) J Biomol NMR 37: 117-135

• PubMed: 17225069 
• DOI: 10.1007/s10858-006-9117-7
• Primary Citation of Related Structures:  
  2NR2


• PubMed Abstract: 
  

While reliable procedures for determining the conformations of proteins are available, methods for generating ensembles of structures that also reflect their flexibility are much less well established. Here we present a systematic assessment of the ability of ensemble-averaged molecular dynamics simulations with ensemble-averaged NMR restraints to simultaneously reproduce the average structure of proteins and their associated dynamics. We discuss the effects that under-restraining (overfitting) and over-restraining (underfitting) have on the structures generated in ensemble-averaged molecular simulations. We then introduce the MUMO (minimal under-restraining minimal over-restraining) method, a procedure in which different observables are averaged over a different number of molecules. As both over-restraining and under-restraining are significantly reduced in the MUMO method, it is possible to generate ensembles of conformations that accurately characterize both the structure and the dynamics of native states of proteins. The application of the MUMO method to the protein ubiquitin yields a high-resolution structural ensemble with an RDC Q-factor of 0.19.

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 144 
• Conformers Submitted: 144 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 2NR2 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-01 
• Released Date: 2007-05-08 
Deposition Author(s): Richter, B., Gsponer, J., Varnai, P., Salvatella, X., Vendruscolo, M.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-16
  Changes: Database references, Derived calculations