2MI8 | pdb_00002mi8

Solution structure of lysine-free (K0) ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb2MI8/pdb
• BMRB: 19670

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


• Deposited: 2013-12-09 Released: 2014-04-02 
• Deposition Author(s): Huang, T., Li, J.R., Byrd, A.R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of lysine-free (K0) ubiquitin.

Huang, T., Li, J., Byrd, R.A.

(2014) Protein Sci 23: 662-667

• PubMed: 24591328 
• DOI: https://doi.org/10.1002/pro.2450
• Primary Citation Related Structures: 
  2MI8


• PubMed Abstract: 
  

  Lysine-free ubiquitin (K0-Ub) is commonly used to study the ubiquitin-signaling pathway, where it is assumed to have the same structure and function as wild-type ubiquitin (wt-Ub). However, the K0-Ub (15) N heteronuclear single quantum correlation NMR spectrum differs significantly from wt-Ub and the melting temperature is depressed by 19°C, raising the question of the structural integrity and equivalence to wt-Ub. The three-dimensional structure of K0-Ub was determined by solution NMR, using chemical shift and residual dipolar coupling data. K0-Ub adopts the same backbone structure as wt-Ub, and all significant chemical shifts can be related to interactions impacted by the K to R mutations.

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Organizational Affiliation: 
• Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.77 kDa 
• Atom Count: 616 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 7  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Huang, T., Li, J.R., Byrd, A.R.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-05-07
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references