SASDBZ6: Draxin

Basic information

• Entry: Database: SASBDB / ID: SASDBZ6

Sample

Draxin

• Draxin (protein), Draxin, Homo sapiens

Function / homology

Function:

commissural neuron differentiation in spinal cord / anterior commissure morphogenesis / dorsal spinal cord development / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / negative regulation of axon extension / forebrain development / axon guidance / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / extracellular region

Domain/homology:

Draxin / Draxin

Component:

Draxin

• Biological species: Homo sapiens (human)
• Citation: Journal: Neuron / Year: 2018; Title: Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC.; Authors: Ying Liu / Tuhin Bhowmick / Yiqiong Liu / Xuefan Gao / Haydyn D T Mertens / Dmitri I Svergun / Junyu Xiao / Yan Zhang / Jia-Huai Wang / Rob Meijers / ; Abstract: Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. VIDEO ABSTRACT.

Contact author

• Haydyn Mertens (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #1747: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1748: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1749: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1750: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1751: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1752: ; Type: mix / Software: (2.1) / Radius of dummy atoms: 1.90 A / Comment: ensemble conformer / Chi-square value: 1.055; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Draxin / Specimen concentration: 0.30-1.20
• Buffer: Name: 20 mM HEPES 150 mM NaCl / pH: 7.5 / Composition: 150 mM NaCl

Entity #431

Name: Draxin / Type: protein / Description: Draxin / Formula weight: 44.5 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q8NBI3
Sequence:

MAGPAIHTAP MLFLVLLLPL ELSLAGALAP GTPARNLPEN HIDLPGPALW TPQASHHRRR GPGKKEWGPG LPSQAQDGAV VTATRQASRL PEAEGLLPEQ SPAGLLQDKD LLLGLALPYP EKENRPPGWE RTRKRSREHK RRRDRLRLHQ GRALVRGPSS LMKKAELSEA QVLDAAMEES STSLAPTMFF LTTFEAAPAT EESLILPVTS LRPQQAQPRS DGEVMPTLDM ALFDWTDYED LKPDGWPSAK KKEKHRGKLS SDGNETSPAE GEPCDHHQDC LPGTCCDLRE HLCTPHNRGL NNKCFDDCMC VEGLRCYAKF HRNRRVTRRK GRCVEPETAN GDQGSFINVG APLEGSENLY FQGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGAHHHHH HHHH

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 1.24 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Draxin / Measurement date: Aug 19, 2015 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.022	4.8204

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1166 /

	Min	Max
Q	0.111917	3.19185
P(R) point	1	1166
R	0	15

Result

Type of curve: merged
Comments: Chemorepulsive axon guidance protein required for the development of spinal cord and forebrain commissures. Acts as a chemorepulsive guidance protein for commissural axons during development. Able to inhibit or repel neurite outgrowth from dorsal spinal cord. Inhibits the stabilization of cytosolic beta-catenin (CTNNB1) via its interaction with LRP6, thereby acting as an antagonist of Wnt signaling pathway

	Experimental	Standard	Standard error	Porod
MW	44 kDa	44 kDa	5	51 kDa
Volume	-	-	-	87 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.03	0.001	0.032	0.001
Radius of gyration, Rg	4.43 nm	0.1	4.2 nm	0.1

	Min	Max	Error
D	-	15	0.5
Guinier point	35	105	-