3B08

Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin

Summary for 3B08

• Entry DOI: 10.2210/pdb3b08/pdb
• Related: 3B0A
• Related PRD ID: PRD_900006
• Descriptor: Polyubiquitin-C, RanBP-type and C3HC4-type zinc finger-containing protein 1, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: protein complex, signaling protein-metal binding protein complex, signaling protein/metal binding protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 8
• Total formula weight: 98597.47

Authors

Sato, Y.,Fujita, H.,Yoshikawa, A.,Yamashita, M.,Yamagata, A.,Kaiser, S.E.,Iwai, K.,Fukai, S. (deposition date: 2011-06-07, release date: 2011-12-14, Last modification date: 2023-11-01)

Primary citation

Sato, Y.,Fujita, H.,Yoshikawa, A.,Yamashita, M.,Yamagata, A.,Kaiser, S.E.,Iwai, K.,Fukai, S.
Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Proc.Natl.Acad.Sci.USA, 108:20520-20525, 2011

PubMed Abstract: The linear ubiquitin chain assembly complex (LUBAC) is a key nuclear factor-κB (NF-κB) pathway component that produces linear polyubiquitin chains. The HOIL-1L subunit of LUBAC has been shown to bind linear chains; however, detailed structural and functional analyses on the binding between LUBAC and linear chains have not been performed. In this study, we found that the Npl4 zinc finger (NZF) domain of HOIL-1L specifically binds linear polyubiquitin chains and determined the crystal structure of the HOIL-1L NZF domain in complex with linear diubiquitin at 1.7-Å resolution. The HOIL-1L NZF domain consists of a zinc-coordinating "NZF core" region and an additional α-helical "NZF tail" region. The HOIL-1L NZF core binds both the canonical Ile44-centered hydrophobic surface on the distal ubiquitin and a Phe4-centered hydrophobic patch on the proximal ubiquitin, representing a mechanism for the specific recognition of linear chains. The NZF tail binds the proximal ubiquitin to enhance the binding affinity. These recognition mechanisms were supported by the accompanying in vitro and in vivo structure-based mutagenesis experiments.

PubMed: 22139374
DOI: 10.1073/pnas.1109088108

Experimental method

X-RAY DIFFRACTION (1.701 Å)