2NBE

Solution structure of V26A mutant of Ubiquitin at pH 2.0

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.1 of the entry. See complete history. 


Literature

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

Surana, P., Das, R.

(2016) Protein Sci 25: 1438-1450

  • DOI: 10.1002/pro.2940
  • Primary Citation of Related Structures:  
    2NBD, 2NBE

  • PubMed Abstract: 

    • The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states ...

    The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process.

    Organizational Affiliation: 

    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
entityA76Homo sapiensMutation(s): 0 
Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2NBE Olderado

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-02-04 
  • Released Date: 2016-05-18 
    • Deposition Author(s): Surana, P., Das, R.

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references