8RNZ | pdb_00008rnz

Metal-binding domain 3 of copper-transporting ATPase RAN1 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism and structural models of protein-mediated copper transfer to the Arabidopsis thaliana ethylene receptor ETR1 at the ER membrane.

Dluhosch, D.Kersten, L.S.Minges, A.Schott-Verdugo, S.Gohlke, H.Groth, G.

(2025) Sci Rep 15: 38501-38501

  • DOI: https://doi.org/10.1038/s41598-025-19915-6
  • Primary Citation of Related Structures:  
    8RNZ

  • PubMed Abstract: 

    In plants, the gaseous plant hormone ethylene regulates a wide range of developmental processes and stress responses. The small unsaturated hydrocarbon is detected by a family of receptors (ETRs) located in the membrane of the endoplasmic reticulum, which rely on a monovalent copper cofactor to detect this hydrocarbon. The copper-transporting P-type ATPase RAN1 (HMA7), located in the same membrane, is known to be essential for the biogenesis of ETRs. Still, the precise molecular mechanism by which the receptors acquire their copper cofactor remains unclear. A recent study by our laboratory demonstrated a direct interaction between RAN1 and soluble copper chaperones of the ATX1 family with the model ethylene receptor ETR1, providing initial insights into the mechanism by which copper is transferred from the cytosol to the membrane-bound receptors. In this study, we further investigated these interactions with respect to the function of individual domains in complex formation. To this end, we combined biochemical experiments and computational predictions and unraveled the processes and mechanisms by which copper is transferred to ETR1 at the molecular level.


  • Organizational Affiliation
    • Institute of Biochemical Plant Physiology, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-transporting ATPase RAN1
A, B
100Arabidopsis thalianaMutation(s): 0 
Gene Names: RAN1HMA7At5g44790K23L20.14T19K24.18
EC: 7.2.2.8
UniProt
Find proteins for Q9S7J8 (Arabidopsis thaliana)
Explore Q9S7J8 
Go to UniProtKB:  Q9S7J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S7J8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.755α = 90
b = 51.481β = 90
c = 62.722γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
DIALSdata reduction
DIALSdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany267205415/CRC 1208

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references
  • Version 1.2: 2025-09-24
    Changes: Database references
  • Version 1.3: 2025-11-19
    Changes: Database references