Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69827.36 
• Atom Count: 4764 
• Residue Count: 622 
• Unique protein chains: 3

5FER

Complex of TRIM25 RING with UbcH5-Ub

• DOI: 10.2210/pdb5FER/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2015-12-17 Released: 2016-05-18 
• Deposition Author(s): Rittinger, K., Koliopoulos, M.G., Esposito, D.
• Funding Organization(s): Medical Research Council (United Kingdom); The Francis Crick Institute 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.273 
• R-Value Work: 0.227 

Literature

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.

Koliopoulos, M.G., Esposito, D., Christodoulou, E., Taylor, I.A., Rittinger, K.

(2016) Embo J. 35: 1204-1218

• PubMed: 27154206 
• DOI: 10.15252/embj.201593741
• Primary Citation of Related Structures:  
  5FEY


• PubMed Abstract: 
  

TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin-loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full-length protein. Our data reveal an unexpected diversity in the self-association mechanism of TRIMs that might be crucial for their biological function.

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Organizational Affiliation: 

Mill Hill Laboratory, Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin/ISG15 ligase TRIM25	A, D	85	Homo sapiens	Mutation(s): 0  Gene Names: TRIM25 (EFP, RNF147, ZNF147) EC: 6.3.2.n3
Find proteins for Q14258 (Homo sapiens) Go to Gene View: TRIM25 Go to UniProtKB:  Q14258

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 D1	B, E	150	Homo sapiens	Mutation(s): 2  Gene Names: UBE2D1 (SFT, UBC5A, UBCH5, UBCH5A) EC: 2.3.2.23
Find proteins for P51668 (Homo sapiens) Go to Gene View: UBE2D1 Go to UniProtKB:  P51668

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-40S ribosomal protein S27a	C, F	76	Bos taurus	Mutation(s): 0  Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus) Go to Gene View: RPS27A Go to UniProtKB:  P62992

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.273 
• R-Value Work: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.480	α = 90.00
b = 71.700	β = 90.00
c = 160.430	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-12-17 
• Released Date: 2016-05-18 
• Deposition Author(s): Rittinger, K., Koliopoulos, M.G., Esposito, D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U117565398
The Francis Crick Institute	United Kingdom	FCI01

Revision History 

• Version 1.0: 2016-05-18
  Type: Initial release
• Version 1.1: 2016-06-15
  Type: Database references
• Version 1.2: 2017-09-13
  Type: Author supporting evidence
• Version 1.3: 2019-02-20
  Type: Advisory, Data collection, Derived calculations