Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 17.37 kDa 
• Atom Count: 1224 
• Residue Count: 149 
• Unique protein chains: 1

3AXC

Crystal structure of linear diubiquitin

• DOI: 10.2210/pdb3AXC/pdb

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


• Deposited: 2011-04-01 Released: 2012-01-25 
• Deposition Author(s): Rohaim, A., Kawasaki, M., Kato, R., Dikic, I., Wakatsuki, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.278 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Structure of a compact conformation of linear diubiquitin

Rohaim, A., Kawasaki, M., Kato, R., Dikic, I., Wakatsuki, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 102-108

• PubMed: 22281738 
• DOI: 10.1107/S0907444911051195
• Primary Citation of Related Structures:  
  3AXC


• PubMed Abstract: 
  

Post-translational modifications involving ubiquitin regulate a wide range of biological processes including protein degradation, responses to DNA damage and immune signalling. Ubiquitin polymerizes into chains which may contain eight different linkage types; the ubiquitin C-terminal glycine can link to one of the seven lysine residues or the N-terminal amino group of methionine in the distal ubiquitin molecule. The latter head-to-tail linkage type, referred to as a linear ubiquitin chain, is involved in NF-κB activation through specific interactions with NF-κB essential modulator (NEMO). Here, a crystal structure of linear diubiquitin at a resolution of 2.2 Å is reported. Although the two ubiquitin moieties do not interact with each other directly, the overall structure adopts a compact but not completely closed conformation with a few intermoiety contacts. This structure differs from the previously reported extended conformation, which resembles Lys63-linked diubiquitin, suggesting that the linear polyubiquitin chain is intrinsically flexible and can adopt multiple conformations.

---

Organizational Affiliation: 

Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	154	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
NIH Common Fund Data Resources
PHAROS:  P62979 GTEx:  ENSG00000143947

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.278 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.261	α = 91.79
b = 35.314	β = 112.85
c = 35.841	γ = 112.88

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-01 
• Released Date: 2012-01-25 
Deposition Author(s): Rohaim, A., Kawasaki, M., Kato, R., Dikic, I., Wakatsuki, S.

Revision History 

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy