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.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 77894.72 
• Atom Count: 4685 
• Residue Count: 698 
• Unique protein chains: 3

5VZW

TRIM23 RING domain in complex with UbcH5-Ub

• DOI: 10.2210/pdb5VZW/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): 2 


• Deposited: 2017-05-29 Released: 2017-08-09 
• Deposition Author(s): Pornillos, O., Dawidziak, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.278 Å
• R-Value Free: 0.237 
• R-Value Work: 0.208 

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

• PubMed: 28681414 
• DOI: 10.1002/prot.25348
• Primary Citation of Related Structures:  
  5VZV


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 D2	A, B	147	Homo sapiens	Mutation(s): 2  Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B) EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens) Go to Gene View: UBE2D2 Go to UniProtKB:  P62837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	C, D	79	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase TRIM23	F, G	123	Homo sapiens	Mutation(s): 0  Gene Names: TRIM23 (ARD1, ARFD1, RNF46) EC: 2.3.2.27
Find proteins for P36406 (Homo sapiens) Go to Gene View: TRIM23 Go to UniProtKB:  P36406

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.278 Å
• R-Value Free: 0.237 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 52.830	α = 90.00
b = 109.355	β = 90.00
c = 122.963	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-29 
• Released Date: 2017-08-09 
• Deposition Author(s): Pornillos, O., Dawidziak, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	R01-GM112508

Revision History 

• Version 1.0: 2017-08-09
  Type: Initial release
• Version 1.1: 2017-09-20
  Type: Database references