Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 18.53 kDa 
• Atom Count: 1352 
• Residue Count: 167 
• Unique protein chains: 2

4Z68

Hybrid structural analysis of the Arp2/3 regulator Arpin identifies its acidic tail as a primary binding epitope

• DOI: 10.2210/pdb4Z68/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-04 Released: 2015-12-30 
• Deposition Author(s): Fetics, S.K., Campanacci, V., Dang, I., Gautreau, A., Cherfils, J.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.217 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 

Literature

Hybrid Structural Analysis of the Arp2/3 Regulator Arpin Identifies Its Acidic Tail as a Primary Binding Epitope.

Fetics, S., Thureau, A., Campanacci, V., Aumont-Nicaise, M., Dang, I., Gautreau, A., Perez, J., Cherfils, J.

(2016) Structure 24: 252-260

• PubMed: 26774128 
• DOI: 10.1016/j.str.2015.12.001
• Primary Citation of Related Structures:  
  4Z68


• PubMed Abstract: 
  

Arpin is a newly discovered regulator of actin polymerization at the cell leading edge, which steers cell migration by exerting a negative control on the Arp2/3 complex. Arpin proteins have an acidic tail homologous to the acidic motif of the VCA domain of nucleation-promoting factors (NPFs). This tail is predicted to compete with the VCA of NPFs for binding to the Arp2/3 complex, thereby mitigating activation and/or tethering of the complex to sites of actin branching. Here, we investigated the structure of full-length Arpin using synchrotron small-angle X-ray scattering, and of its acidic tail in complex with an ankyrin repeats domain using X-ray crystallography. The data were combined in a hybrid model in which the acidic tail extends from the globular core as a linear peptide and forms a primary epitope that is readily accessible in unbound Arpin and suffices to tether Arpin to interacting proteins with high affinity.

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Organizational Affiliation: 

Laboratoire de Pharmacologie et Biologie Appliquée, UMR 8113, CNRS-Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan Cedex, France; Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, 91190 Gif-sur-Yvette, France. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	A	155	Homo sapiens	Mutation(s): 0  Gene Names: TNKS2, PARP5B, TANK2, TNKL EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for Q9H2K2 (Homo sapiens) Explore Q9H2K2  Go to UniProtKB:  Q9H2K2
NIH Common Fund Data Resources
PHAROS:  Q9H2K2 GTEx:  ENSG00000107854

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-ILE-ARG-GLU-GLN-GLY-ASP-GLY-ALA-GLU-ASP-GLU	E	12	Homo sapiens	Mutation(s): 0  Gene Names: ARPIN, C15orf38
Find proteins for Q7Z6K5 (Homo sapiens) Explore Q7Z6K5  Go to UniProtKB:  Q7Z6K5
NIH Common Fund Data Resources
PHAROS:  Q7Z6K5 GTEx:  ENSG00000242498

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.217 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.543	α = 90
b = 43.806	β = 90
c = 107.637	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-04 
• Released Date: 2015-12-30 
Deposition Author(s): Fetics, S.K., Campanacci, V., Dang, I., Gautreau, A., Cherfils, J.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History 

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence