Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8192.38 
• Atom Count: 575 
• Residue Count: 72 
• Unique protein chains: 1

3ONS

Crystal structure of Human Ubiquitin in a new crystal form

• DOI: 10.2210/pdb3ONS/pdb

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


• Deposited: 2010-08-30 Released: 2011-02-23 
• Deposition Author(s): Amodeo, G.A., Huang, K.Y., Mcdermott, A.E., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 

Literature

The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch.

Huang, K.Y., Amodeo, G.A., Tong, L., McDermott, A.

(2011) Protein Sci. 20: 630-639

• PubMed: 21432937 
• DOI: 10.1002/pro.584


• PubMed Abstract: 
  

A new crystal structure of human ubiquitin is reported at 1.8 Å resolution. Compared with the other known crystal structure or the solution NMR structure of monomeric human ubiquitin, this new structure is similar in its overall fold but differs with respect to the conformation of the backbone in a surface-exposed region. The conformation reported here resembles conformations previously seen in complex with deubiquinating enzymes, wherein the Asp52/Gly53 main chain and Glu24 side chain move. This movement exposes the backbone carbonyl of Asp52 to the exterior of the molecule, making it possible to engage in hydrogen-bond contacts with neighboring molecules, rather than in an internal hydrogen bond with the backbone of Glu24. This particular crystal form of ubiquitin has been used in a large number of solid state NMR studies. The structure described here elucidates the origin of many of the chemical shift differences comparing solution and solid state studies.

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Organizational Affiliation: 

Department of Chemistry, Columbia University, New York, New York 10027, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	A	72	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: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 48.410	α = 90.00
b = 48.410	β = 90.00
c = 61.970	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
COMO	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-30 
• Released Date: 2011-02-23 
• Deposition Author(s): Amodeo, G.A., Huang, K.Y., Mcdermott, A.E., Tong, L.

Revision History 

• Version 1.0: 2011-02-23
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-08-10
  Type: Database references