9Q88 | pdb_00009q88

High-resolution structure of RNF38 RING domain

• PDB DOI: https://doi.org/10.2210/pdb9Q88/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-23 Released: 2025-07-30 
• Deposition Author(s): Gabrielsen, M., Buetow, L., Huang, D.T.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.168 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.151 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Tuning ubiquitin transfer by RING E3 ubiquitin ligases through the linchpin residue.

Nakasone, M.A., Buetow, L., Gabrielsen, M., Ahmed, S.F., Majorek, K.A., Sibbet, G.J., Smith, B.O., Huang, D.T.

(2025) Life Sci Alliance 8

• PubMed: 40763985 
• DOI: https://doi.org/10.26508/lsa.202503394
• Primary Citation Related Structures: 
  9Q88, 9Q8Y


• PubMed Abstract: 
  

  RING family ubiquitin ligases (E3s) employ the RING domain to recruit the E2 thioester ubiquitin (E2∼Ub) intermediate to catalyze the transfer of ubiquitin (Ub) to substrates. A cationic Arg linchpin (LP) residue in the RING domain plays a key role in stabilizing the interface with E2∼Ub, but the identity of the LP residue varies across E3s. Here, we investigate how the LP residue contributes to ubiquitination. Using the model RNF38 system, we demonstrate that substitution of LP ^Arg to the other 19 available amino acids modulates ubiquitination, ranging from minor reduction to complete abolition. The identity of the LP residue influences E2∼Ub binding but does not correlate with E3 activity. NMR and X-ray crystallography analyses reveal that RNF38 LP ^Arg variants stabilize E2∼Ub in a catalytically competent conformation to varying degrees. By altering the LP residue in XIAP, we show that the XIAP ^Y485R variant promotes E2∼Ub stabilization and enhances substrate ubiquitination in cells. Our work demonstrates the importance of the LP residue in modulating E2∼Ub conformation to control ubiquitination.

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Organizational Affiliation: 
• Cancer Research UK Scotland Institute, Glasgow, UK [e-mail].
Cancer Research UK Scotland Institute, Glasgow, UK.
School of Molecular Biosciences, University of Glasgow, Glasgow, UK.
Cancer Research UK Scotland Institute, Glasgow, UK [e-mail].
School of Cancer Sciences, University of Glasgow, Glasgow, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.27 kDa 
• Atom Count: 741 
• Modeled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF38	A	79	Homo sapiens	Mutation(s): 0  Gene Names: RNF38 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0F5 (Homo sapiens) Explore Q9H0F5  Go to UniProtKB:  Q9H0F5
PHAROS:  Q9H0F5 GTEx:  ENSG00000137075

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.168 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.151 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.82	α = 90
b = 39.309	β = 90
c = 53.208	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Gabrielsen, M., Buetow, L., Huang, D.T.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2025-08-20
  Changes: Database references