6W9A

RNF12 RING domain in complex with Ube2e2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains.

Middleton, A.J.Zhu, J.Day, C.L.

(2020) J Mol Biol 432: 3790-3801

  • DOI: https://doi.org/10.1016/j.jmb.2020.05.001
  • Primary Citation of Related Structures:  
    6W7Z, 6W9A, 6W9D

  • PubMed Abstract: 
  • RNF12 is a widely expressed ubiquitin E3 ligase that is required for X-chromosome inactivation, regulation of LIM-domain containing transcription factors, and TGF-β signaling. A RING domain at the C terminus of RNF12 is important for its E3 ligase activity, and mutations in the RING domain are associated with X-linked intellectual disability ...

    RNF12 is a widely expressed ubiquitin E3 ligase that is required for X-chromosome inactivation, regulation of LIM-domain containing transcription factors, and TGF-β signaling. A RING domain at the C terminus of RNF12 is important for its E3 ligase activity, and mutations in the RING domain are associated with X-linked intellectual disability. Here we have characterized ubiquitin transfer by RNF12, and show that the RING domain can bind to, and is active with, ubiquitin conjugating enzymes (E2s) that produce degradative ubiquitin chains. We report the crystal structures of RNF12 in complex with two of these E2 enzymes, as well as with an E2~Ub conjugate in a closed conformation. These structures form a basis for understanding the deleterious effect of a number of disease causing mutations. Comparison of the RNF12 structure with other monomeric RINGs suggests that a loop prior to the core RING domain has a conserved and essential role in stabilization of the active conformation of the bound E2~Ub conjugate. Together these findings provide a framework for better understanding substrate ubiquitylation by RNF12 and the impact of disease causing mutations.


    Organizational Affiliation

    Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand. Electronic address: catherine.day@otago.ac.nz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 E2A, C177Homo sapiensMutation(s): 0 
Gene Names: UBE2E2UBCH8
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LR5 (Homo sapiens)
Explore Q96LR5 
Go to UniProtKB:  Q96LR5
PHAROS:  Q96LR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LR5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RLIMB, D98Homo sapiensMutation(s): 0 
Gene Names: RLIMRNF12
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVW2 (Homo sapiens)
Explore Q9NVW2 
Go to UniProtKB:  Q9NVW2
PHAROS:  Q9NVW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVW2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.355α = 90
b = 81.355β = 90
c = 98.247γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references