5VZW

TRIM23 RING domain in complex with UbcH5-Ub

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase.

Dawidziak, D.M., Sanchez, J.G., Wagner, J.M., Ganser-Pornillos, B.K., Pornillos, O.

(2017) Proteins 85: 1957-1961

  • DOI: 10.1002/prot.25348
  • Primary Citation of Related Structures:  
    5VZV, 5VZW

  • PubMed Abstract: 

    • Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains ...

    Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2-ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

    Organizational Affiliation: 

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2A,
E [auth B]		147Homo sapiensMutation(s): 2 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
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UniProt GroupP62837
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB [auth C],
F [auth D]		79Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Entity Groups  
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UniProt GroupP0CG47
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM23C [auth F],
D [auth G]		123Homo sapiensMutation(s): 0 
Gene Names: TRIM23, ARD1, ARFD1, RNF46
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P36406 (Homo sapiens)
Explore P36406 
Go to UniProtKB:  P36406
PHAROS:  P36406
GTEx:  ENSG00000113595 
Entity Groups  
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UniProt GroupP36406
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.83α = 90
b = 109.355β = 90
c = 122.963γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM112508

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence