6S53

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MPDClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NA [auth E],
C,
G [auth K],
I
152Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61088
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-CB [auth F],
D,
H [auth L],
J
76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21E [auth B],
F [auth A],
K [auth H],
L [auth G]
85Homo sapiensMutation(s): 0 
Gene Names: TRIM21RNF81RO52SSA1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19474
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
Q [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
M [auth B]
N [auth B]
O [auth A]
P [auth A]
R [auth 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 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.75α = 89.9
b = 83.31β = 89.05
c = 86.75γ = 88.7
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MPDClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105181010
Medical Research Council (United Kingdom)United KingdomU105178934
Wellcome TrustUnited KingdomInvestigator Award to Leo C James

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description