5D0I | pdb_00005d0i

Structure of RING finger protein 165

• PDB DOI: https://doi.org/10.2210/pdb5D0I/pdb

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


• Deposited: 2015-08-03 Released: 2015-12-09 
• Deposition Author(s): Wright, J.D., Day, C.L., Mace, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.

Wright, J.D., Mace, P.D., Day, C.L.

(2016) Nat Struct Mol Biol 23: 45-52

• PubMed: 26656854 
• DOI: https://doi.org/10.1038/nsmb.3142
• Primary Citation Related Structures: 
  5D0I, 5D0K, 5D0M


• PubMed Abstract: 
  

  RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.

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Organizational Affiliation: 
• Biochemistry Department, University of Otago, Dunedin, New Zealand.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.39 kDa 
• Atom Count: 963 
• Modeled Residue Count: 113 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein 165	A, B	97	Homo sapiens	Mutation(s): 0  Gene Names: RNF165 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZSG1 (Homo sapiens) Explore Q6ZSG1  Go to UniProtKB:  Q6ZSG1
PHAROS:  Q6ZSG1 GTEx:  ENSG00000141622

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.22	α = 90
b = 76.22	β = 90
c = 103.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Wright, J.D., Day, C.L., Mace, P.D.

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2015-12-30
  Changes: Database references
• Version 1.2: 2016-01-20
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations