3DVG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 

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, 3DVG

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Human IgG1 fab fragment light chainA217Homo sapiensMutation(s): 0 
Gene Names: fab fragment light chainIGK@
Find proteins for Q6PIL8 (Homo sapiens)
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Go to UniProtKB:  Q6PIL8
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Human IgG1 fab fragment heavy chainB230Homo sapiensMutation(s): 0 
Gene Names: fab fragment light chain
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin D77X80Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1UBA52UBCEP2UBBUBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinY79Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1UBA52UBCEP2UBBUBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.806α = 90
b = 88.117β = 108.28
c = 90.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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
    Changes: Advisory, Refinement description, Version format compliance