Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.89 kDa 
• Atom Count: 4736 
• Residue Count: 601 
• 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): Yes 


• 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 (NIH/NIGMS)

---

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 

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, 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
NIH Common Fund Data Resources
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D	79	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P36406  Go to UniProtKB:  P36406
NIH Common Fund Data Resources
PHAROS:  P36406 GTEx:  ENSG00000113595

Small Molecules

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

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 = 52.83	α = 90
b = 109.355	β = 90
c = 122.963	γ = 90

Software Package:

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

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.

---

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

Revision History 

• 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