7BVW | pdb_00007bvw

Crystal structure of the RING-H2 domain of Arabidopsis RMR1

• PDB DOI: https://doi.org/10.2210/pdb7BVW/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-12 Released: 2021-04-14 
• Deposition Author(s): Chen, S., Wong, K.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The RING-finger domain of Arabidopsis RMR functions as an E3 ligase essential for post-Golgi trafficking.

Chen, S., Zeng, Y.L., Wong, H.Y., Chen, Y.H., Yang, L., Luo, F., Gao, C.J., Jiang, L.W., Wong, K.B.

(2025) J Biological Chem 

• DOI: https://doi.org/10.1016/j.jbc.2025.110721

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.79 kDa 
• Atom Count: 1,263 
• Modeled Residue Count: 154 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT5G66160 protein	A, B	82	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g66160
UniProt
Find proteins for Q9M622 (Arabidopsis thaliana) Explore Q9M622  Go to UniProtKB:  Q9M622

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.431	α = 90
b = 23.648	β = 94.8
c = 75.699	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Chen, S., Wong, K.B.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-09-24
  Changes: Database references, Structure summary