SASDBV2: Zebrafish Arpin (Zebrafish (Danio rerio) Arpin, Arpin)

Basic information

Entry

Database: SASBDB / ID: SASDBV2

Sample

Zebrafish Arpin

• Zebrafish (Danio rerio) Arpin (protein), Arpin, Danio rerio

• Function / homology: Arpin / Arp2/3-interacting proteins Arpin / negative regulation of actin nucleation / directional locomotion / negative regulation of cell migration / lamellipodium / Arpin
• Biological species: Danio rerio (zebrafish)
• Citation: Journal: Structure / Year: 2016; Title: Hybrid Structural Analysis of the Arp2/3 Regulator Arpin Identifies Its Acidic Tail as a Primary Binding Epitope.; Authors: Susan Fetics / Aurélien Thureau / Valérie Campanacci / Magali Aumont-Nicaise / Irène Dang / Alexis Gautreau / Javier Pérez / Jacqueline Cherfils / ; 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.

Contact author

• Aurélien Thureau (Soleil, Soleil Synchrotron, Saint-Aubin, France)

Models

Sample

• Sample: Name: Zebrafish Arpin
• Buffer: Name: 50 mM HEPES 100mM NaCl 1mM TCEP / Concentration: 50.00 mM / pH: 7.5 / Composition: 100mM NaCl, 1mM TCEP

Entity #276

Name: Arpin / Type: protein / Description: Zebrafish (Danio rerio) Arpin / Formula weight: 25.471 / Num. of mol.: 1 / Source: Danio rerio / References: UniProt: Q1LWJ6
Sequence:

GSRIYDNTAL LNKPVHNEKL SFTWDPIVHQ SGHGVILEGT VVDFSRHAIT DVKNRKERYN VLYIKPSRVH RRKYDSKGNE IEPNFSDTKK VNTGFLMSSF KVEAKGETDC LDERQLREIV NKEQLVKVTI KHCPREAFAF WISEAEMDKT ELEPGQEVRL KTKGDGPFIF SSAKLDSGTV TKCNFAGDEN AGASWTEKIM ANKSNQENTG KSAAQGEGAD DDEWDD

Experimental information

• Beam: Instrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 1.82 mm
• Detector: Name: AVIEX PCCD170170 / Type: CCD

Scan

Title: Zebrafish Arpin / Measurement date: Dec 4, 2014 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 1.5 sec. / Unit: 1/nm /

	Min	Max
Q	0.062	6.0833

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 591 /

	Min	Max
Q	0.112661	3.43208
P(R) point	1	591
R	0	13.8

Result

Type of curve: single_conc
Comments: Due to high concentration at the elution peak, the HPLC UV detector was saturated and the concentrations of the sample was consequently underestimated. In this case, the molecular mass is overestimated when assessing this parameter from I(0) and concentration.

	Experimental	Porod
MW	30.8 kDa	-
Volume	-	46.6 nm3

	P(R)	Guinier	P(R) error
Forward scattering, I0	0.04	0.041	-
Radius of gyration, Rg	2.79 nm	2.69 nm	0.04

	Min	Max
D	-	13.8
Guinier point	9	83