5ZD0

Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 4400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report



Literature

High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.

Tanaka, T.Ikeya, T.Kamoshida, H.Suemoto, Y.Mishima, M.Shirakawa, M.Guntert, P.Ito, Y.

(2019) Angew Chem Int Ed Engl 58: 7284-7288

  • DOI: 10.1002/anie.201900840
  • Primary Citation of Related Structures:  
    5Z4B, 5ZCZ, 5ZD0

  • PubMed Abstract: 
  • Proteins in living cells interact specifically or nonspecifically with an enormous number of biomolecules. To understand the behavior of proteins under intracellular crowding conditions, it is indispensable to observe their three-dimensional (3D) structu ...

    Proteins in living cells interact specifically or nonspecifically with an enormous number of biomolecules. To understand the behavior of proteins under intracellular crowding conditions, it is indispensable to observe their three-dimensional (3D) structures at the atomic level in a physiologically natural environment. We demonstrate the first de novo protein structure determinations in eukaryotes with the sf9 cell/baculovirus system using NMR data from living cells exclusively. The method was applied to five proteins, rat calmodulin, human HRas, human ubiquitin, T. thermophilus HB8 TTHA1718, and Streptococcus protein G B1 domain. In all cases, we could obtain structural information from well-resolved in-cell 3D nuclear Overhauser effect spectroscopy (NOESY) data, suggesting that our method can be a standard tool for protein structure determinations in living eukaryotic cells. For three proteins, we achieved well-converged 3D structures. Among these, the in-cell structure of protein G B1 domain was most accurately determined, demonstrating that a helix-loop region is tilted away from a β-sheet compared to the conformation in diluted solution.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitin A76Homo sapiensMutation(s): 3 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 4400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • OLDERADO: 5ZD0 Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanCREST; JPMJCR13M3

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release