9JJX | pdb_00009jjx

Truncated RNF112, GDP-bound form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.293 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: in silico
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Literature

Structural and functional characterization of the brain-specific dynamin superfamily member RNF112.

Zhong, Y.T.Huang, L.L.Li, K.Yang, B.Ye, X.Zhong, H.R.Yu, B.Ma, M.Yuan, Y.Meng, Y.Pan, R.Zhang, H.Shi, L.Wang, Y.Tian, R.Gao, S.Bian, X.

(2025) Proc Natl Acad Sci U S A 122: e2419449122-e2419449122

  • DOI: https://doi.org/10.1073/pnas.2419449122
  • Primary Citation of Related Structures:  
    9JJU, 9JJV, 9JJW, 9JJX

  • PubMed Abstract: 

    Most members of the dynamin superfamily of large guanosine triphophatases (GTPases) have an ability to remodel membranes in response to guanosine triphosphate (GTP) hydrolysis. Ring Finger Protein 112 (RNF112) (ZNF179/neurolastin) is a recently identified brain-specific dynamin-like protein possessing a really interesting new gene (RING) finger domain. Despite its essential role as an E3 ligase in neuron development, the architecture of RNF112 and the exact role of its GTPase activity remain unknown. Here, we determined the crystal structure of truncated RNF112 (RNF112 T ) containing a GTPase domain (GD) and three-helical middle domain (MD) at different nucleotide-loading states. In the nucleotide-free (apo) state, the monomeric RNF112 T remained in a unique self-restraint conformation characterized by docking of the proximal end of the MD to a groove in the GD. At the transition state of GTP hydrolysis, the MD was released from the GD and stretched aside to form an intertwined RNF112 T homodimer. Engineered RNF112 equipped with the C-terminal elements of ATL1 or the two transmembrane domains of yeast Sac1p relocated to the endoplasmic reticulum and was capable of mediating membrane remodeling. Taken together, our results offer necessary understandings of RNF112 as a dynamin-like large GTPase in its cellular function and provide insights into the functional mechanisms of dynamin superfamily proteins.


  • Organizational Affiliation
    • Guangdong Provincial Clinical Research Center for Cancer, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LOC432253 protein
A, B
399Xenopus laevisMutation(s): 0 
Gene Names: rnf112.LLOC432253rnf112rnf112.Sznf179
UniProt
Find proteins for Q2VPQ0 (Xenopus laevis)
Explore Q2VPQ0 
Go to UniProtKB:  Q2VPQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VPQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.39α = 96.44
b = 48.387β = 96.25
c = 124.029γ = 90.42
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32320103002
National Natural Science Foundation of China (NSFC)China82173098

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release