9Z8N | pdb_00009z8n

Crystal structure of RNF14 RING2 domain bound to K6/K48 branched tri-ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb9Z8N/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-11-18 Released: 2026-11-11 
• Deposition Author(s): Trevelyan, S.J., Lechtenberg, B.C.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.270 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Models: in silico, experimental

Literature

The C-terminal tail of the RBR E3 ligase RNF14 defines branched K6/K48 polyubiquitin specificity in ribosomal quality control

Trevelyan, S.J., Riedel, J., Tong, Y.H., Dong, H., Jiou, J., McGowan, E.N.S., Wang, X.S., Cobbold, S.A., Feltham, R., Lechtenberg, B.C.

(2026) Mol Cell 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 80.99 kDa 
• Atom Count: 5,127 
• Modeled Residue Count: 642 
• Deposited Residue Count: 706 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF14	A, B	126	Homo sapiens	Mutation(s): 1  Gene Names: RNF14, ARA54, HRIHFB2038 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBS8 (Homo sapiens) Explore Q9UBS8  Go to UniProtKB:  Q9UBS8
PHAROS:  Q9UBS8 GTEx:  ENSG00000013561

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D, G, H	76	Homo sapiens	Mutation(s): 2  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	E, F	75	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.270 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.619	α = 90
b = 189.868	β = 90
c = 121.515	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Trevelyan, S.J., Lechtenberg, B.C.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1182757
National Health and Medical Research Council (NHMRC, Australia)	Australia	2016268

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release