3AXC

Crystal structure of linear diubiquitin


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin154Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens)
Explore P62979 
Go to UniProtKB:  P62979
GTEx:  ENSG00000143947 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62979
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth 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 = 33.261α = 91.79
b = 35.314β = 112.85
c = 35.841γ = 112.88
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description