Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, homology

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 141.49 kDa 
• Atom Count: 9476 
• Residue Count: 1214 
• Unique protein chains: 3

6S53

Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate

• DOI: 10.2210/pdb6S53/pdb

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


• Deposited: 2019-06-30 Released: 2019-09-11 
• Deposition Author(s): Kiss, L., Boland, A., Neuhaus, D., James, L.C.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.209 

Literature

A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases.

Kiss, L., Zeng, J., Dickson, C.F., Mallery, D.L., Yang, J.C., McLaughlin, S.H., Boland, A., Neuhaus, D., James, L.C.

(2019) Nat Commun 10: 4502-4502

• PubMed: 31582740 
• DOI: 10.1038/s41467-019-12388-y
• Primary Citation of Related Structures:  
  6S53


• PubMed Abstract: 
  

The cytosolic antibody receptor TRIM21 possesses unique ubiquitination activity that drives broad-spectrum anti-pathogen targeting and underpins the protein depletion technology Trim-Away. This activity is dependent on formation of self-anchored, K63-linked ubiquitin chains by the heterodimeric E2 enzyme Ube2N/Ube2V2. Here we reveal how TRIM21 facilitates ubiquitin transfer and differentiates this E2 from other closely related enzymes. A tri-ionic motif provides optimally distributed anchor points that allow TRIM21 to wrap an Ube2N~Ub complex around its RING domain, locking the closed conformation and promoting ubiquitin discharge. Mutation of these anchor points inhibits ubiquitination with Ube2N/Ube2V2, viral neutralization and immune signalling. We show that the same mechanism is employed by the anti-HIV restriction factor TRIM5 and identify spatially conserved ionic anchor points in other Ube2N-recruiting RING E3s. The tri-ionic motif is exclusively required for Ube2N but not Ube2D1 activity and provides a generic E2-specific catalysis mechanism for RING E3s.

---

Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	C, E, I, K	152	Homo sapiens	Mutation(s): 0  Gene Names: UBE2N, BLU EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088 GTEx:  ENSG00000177889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	D, F, J, L	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS:  P0CG48

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A, B, G, H	85	Homo sapiens	Mutation(s): 0  Gene Names: TRIM21, RNF81, RO52, SSA1 EC: 2.3.2.27
Find proteins for P19474 (Homo sapiens) Explore P19474  Go to UniProtKB:  P19474
NIH Common Fund Data Resources
PHAROS:  P19474 GTEx:  ENSG00000132109

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	A, B, G, H	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.209 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.75	α = 89.9
b = 83.31	β = 89.05
c = 86.75	γ = 88.7

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-06-30 
• Released Date: 2019-09-11 
Deposition Author(s): Kiss, L., Boland, A., Neuhaus, D., James, L.C.

---

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105181010
Medical Research Council (United Kingdom)	United Kingdom	U105178934
Wellcome Trust	United Kingdom	Investigator Award to Leo C James

Revision History 

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references