3ZLZ

Lys6-linked tri-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Assembly, Analysis and Architecture of Atypical Ubiquitin Chains

Hospenthal, M.K.Freund, S.M.V.Komander, D.

(2013) Nat.Struct.Mol.Biol. 20: 555

  • DOI: 10.1038/nsmb.2547

  • PubMed Abstract: 
  • Ubiquitin (Ub) chains regulate many cellular processes, but several chain types including Lys6 linkages have remained unstudied. Here we analyze the bacterial effector E3 ligase NleL (non-Lee-encoded effector ligase) from enterohemorrhagic Escherichi ...

    Ubiquitin (Ub) chains regulate many cellular processes, but several chain types including Lys6 linkages have remained unstudied. Here we analyze the bacterial effector E3 ligase NleL (non-Lee-encoded effector ligase) from enterohemorrhagic Escherichia coli (EHEC) O157:H7, which assembles Lys6- and Lys48-linked Ub polymers. Using linkage-specific human deubiquitinases (DUBs) we show that NleL generates heterotypic Ub chains, and branched chains are efficiently hydrolyzed by DUBs. USP family DUBs cleave Lys6-linked polymers exclusively from the distal end, whereas a DUB with preference for Lys6 can cleave Lys6-linked polymers at any position in the chain. We used NleL to generate large quantities of Lys6-linked polyUb. Crystallographic and NMR spectroscopy analyses revealed that an asymmetric interface between Ile44 and Ile36 hydrophobic patches of neighboring Ub moieties is propagated in longer Lys6-linked Ub chains. Interactions via the Ile36 patch can displace Leu8 from the Ile44 patch, leading to marked structural perturbations of Ub.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN
A, B
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 104.930α = 90.00
b = 104.930β = 90.00
c = 104.930γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2013-05-22
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Data collection