3V3L

Crystal structure of human RNF146 WWE domain in complex with iso-ADPRibose

• PDB DOI: https://doi.org/10.2210/pdb3V3L/pdb

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


• Deposited: 2011-12-13 Released: 2012-02-15 
• Deposition Author(s): Wang, Z., Cheng, Z., Xu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Recognition of the iso-ADP-ribose moiety in poly(ADP-ribose) by WWE domains suggests a general mechanism for poly(ADP-ribosyl)ation-dependent ubiquitination.

Wang, Z., Michaud, G.A., Cheng, Z., Zhang, Y., Hinds, T.R., Fan, E., Cong, F., Xu, W.

(2012) Genes Dev 26: 235-240

• PubMed: 22267412 
• DOI: https://doi.org/10.1101/gad.182618.111
• Primary Citation of Related Structures:  
  3V3L


• PubMed Abstract: 
  

  Protein poly(ADP-ribosyl)ation and ubiquitination are two key post-translational modifications regulating many biological processes. Through crystallographic and biochemical analysis, we show that the RNF146 WWE domain recognizes poly(ADP-ribose) (PAR) by interacting with iso-ADP-ribose (iso-ADPR), the smallest internal PAR structural unit containing the characteristic ribose-ribose glycosidic bond formed during poly(ADP-ribosyl)ation. The key iso-ADPR-binding residues we identified are highly conserved among WWE domains. Binding assays further demonstrate that PAR binding is a common function for the WWE domain family. Since many WWE domain-containing proteins are known E3 ubiquitin ligases, our results suggest that protein poly(ADP-ribosyl)ation may be a general mechanism to target proteins for ubiquitination.

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Organizational Affiliation: 

Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 21.63 kDa 
• Atom Count: 1,722 
• Modelled Residue Count: 168 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF146	A, B	85	Homo sapiens	Mutation(s): 0  Gene Names: RNF146 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTX7 (Homo sapiens) Explore Q9NTX7  Go to UniProtKB:  Q9NTX7
PHAROS:  Q9NTX7 GTEx:  ENSG00000118518

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V3L	C [auth A], D [auth B]	2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) C15 H23 N5 O14 P2 BHIWBSNWEZIHHL-KEOHHSTQSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.343	α = 90
b = 55.343	β = 90
c = 146.471	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Wang, Z., Cheng, Z., Xu, W.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary