6S53

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.Boland, A.Neuhaus, D.James, L.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
E, C, K, I
152Homo sapiensMutation(s): 0 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
F, D, L, J
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase TRIM21
B, A, H, G
85Homo sapiensMutation(s): 0 
Gene Names: TRIM21 (RNF81, RO52, SSA1)
EC: 2.3.2.27
Find proteins for P19474 (Homo sapiens)
Go to Gene View: TRIM21
Go to UniProtKB:  P19474
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.750α = 89.90
b = 83.310β = 89.05
c = 86.750γ = 88.70
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-09-11
    Type: Initial release