6W9D

RNF12 RING domain in complex with a Ube2d2~Ub conjugate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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: 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2A, D, G155Homo sapiensMutation(s): 5 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RLIMB, E, H98Homo sapiensMutation(s): 0 
Gene Names: RLIM, RNF12
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
GTEx:  ENSG00000131263
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinC, F, I76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.473α = 90
b = 135.473β = 90
c = 51.372γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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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