5FER

Complex of TRIM25 RING with UbcH5-Ub

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history. 


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

  • DOI: 10.15252/embj.201593741
  • Primary Citation of Related Structures:  
    5FER, 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 ...

    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.

    Organizational Affiliation: 

    Mill Hill Laboratory, Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK katrin.rittinger@crick.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin/ISG15 ligase TRIM25A, D85Homo sapiensMutation(s): 0 
Gene Names: TRIM25, EFP, RNF147, ZNF147
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
Find proteins for Q14258 (Homo sapiens)
Explore Q14258 
Go to UniProtKB:  Q14258
NIH Common Fund Data Resources
PHAROS:  Q14258
GTEx:  ENSG00000121060
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D1B, E150Homo sapiensMutation(s): 2 
Gene Names: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
Find proteins for P51668 (Homo sapiens)
Explore P51668 
Go to UniProtKB:  P51668
NIH Common Fund Data Resources
PHAROS:  P51668
GTEx:  ENSG00000072401
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aC, F76Bos taurusMutation(s): 0 
Gene Names: RPS27A, UBA80, UBCEP1
Find proteins for P62992 (Bos taurus)
Explore P62992 
Go to UniProtKB:  P62992
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.48α = 90
b = 71.7β = 90
c = 160.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU117565398
The Francis Crick InstituteUnited KingdomFCI01

Revision History  (Full details and data files)

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