3DVG

Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.

Newton, K.Matsumoto, M.L.Wertz, I.E.Kirkpatrick, D.S.Lill, J.R.Tan, J.Dugger, D.Gordon, N.Sidhu, S.S.Fellouse, F.A.Komuves, L.French, D.M.Ferrando, R.E.Lam, C.Compaan, D.Yu, C.Bosanac, I.Hymowitz, S.G.Kelley, R.F.Dixit, V.M.

(2008) Cell 134: 668-678

  • DOI: 10.1016/j.cell.2008.07.039
  • Primary Citation of Related Structures:  3DVN

  • PubMed Abstract: 
  • Posttranslational modification of proteins with polyubiquitin occurs in diverse signaling pathways and is tightly regulated to ensure cellular homeostasis. Studies employing ubiquitin mutants suggest that the fate of polyubiquitinated proteins is det ...

    Posttranslational modification of proteins with polyubiquitin occurs in diverse signaling pathways and is tightly regulated to ensure cellular homeostasis. Studies employing ubiquitin mutants suggest that the fate of polyubiquitinated proteins is determined by which lysine within ubiquitin is linked to the C terminus of an adjacent ubiquitin. We have developed linkage-specific antibodies that recognize polyubiquitin chains joined through lysine 63 (K63) or 48 (K48). A cocrystal structure of an anti-K63 linkage Fab bound to K63-linked diubiquitin provides insight into the molecular basis for specificity. We use these antibodies to demonstrate that RIP1, which is essential for tumor necrosis factor-induced NF-kappaB activation, and IRAK1, which participates in signaling by interleukin-1beta and Toll-like receptors, both undergo polyubiquitin editing in stimulated cells. Both kinase adaptors initially acquire K63-linked polyubiquitin, while at later times K48-linked polyubiquitin targets them for proteasomal degradation. Polyubiquitin editing may therefore be a general mechanism for attenuating innate immune signaling.


    Organizational Affiliation

    Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Human IgG1 fab fragment light chain
A
217Homo sapiensGene Names: IGK@
Find proteins for Q6PIL8 (Homo sapiens)
Go to UniProtKB:  Q6PIL8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Human IgG1 fab fragment heavy chain
B
230N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin D77
X
80Homo sapiensGene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
Y
79Homo sapiensGene 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: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.806α = 90.00
b = 88.117β = 108.28
c = 90.226γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-07-18 
  • Released Date: 2008-09-30 
  • Deposition Author(s): Hymowitz, S.G.

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance