6YXE | pdb_00006yxe

Structure of the Trim69 RING domain

• PDB DOI: https://doi.org/10.2210/pdb6YXE/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-01 Released: 2020-10-14 
• Deposition Author(s): Keown, J.R., Goldstone, D.C.
• Funding Organization(s): Marsden Fund, Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The RING domain of TRIM69 promotes higher-order assembly.

Keown, J.R., Yang, J., Black, M.M., Goldstone, D.C.

(2020) Acta Crystallogr D Struct Biol 76: 954-961

• PubMed: 33021497 
• DOI: https://doi.org/10.1107/S2059798320010499
• Primary Citation Related Structures: 
  6YXE


• PubMed Abstract: 
  

  Members of the TRIM protein family have been shown to inhibit a range of viral infections. Recently, TRIM69 was identified as a potent inhibitor of Vesicular stomatitis Indiana virus infection, with its inhibition being dependent upon multimerization. Using SEC-MALLS analysis, it is demonstrated that the assembly of TRIM69 is mediated through the RING domain and not the Bbox domain as has been shown for other TRIM proteins. Using X-ray crystallography, the structure of the TRIM69 RING domain has been determined to a resolution of 2.1 Å, the oligomerization interface has been identified and regions outside the four-helix bundle have been observed to form interactions that are likely to support assembly.

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Organizational Affiliation: 
• School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 29.74 kDa 
• Atom Count: 1,331 
• Modeled Residue Count: 161 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM69	A, B	128	Homo sapiens	Mutation(s): 0  Gene Names: TRIM69, RNF36, HSD-34, HSD34 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WT6 (Homo sapiens) Explore Q86WT6  Go to UniProtKB:  Q86WT6
PHAROS:  Q86WT6 GTEx:  ENSG00000185880

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.965	α = 90
b = 109.965	β = 90
c = 90.135	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
SHELXDE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Keown, J.R., Goldstone, D.C.

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Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	--
Royal Society of New Zealand	New Zealand	--

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Refinement description