4xhq

From Proteopedia

(Difference between revisions)

Current revision

Re-refinement the crystal structure of Dscam1 isoform 1.34, N-terminal four Ig domains

Structural highlights

4xhq is a 1 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.948Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DSCA1_DROME Cell surface receptor involved in guidance and targeting of growing nerve axons (PubMed:10892653). Required during Bolwig's organ differentiation for accurate and efficient targeting of photoreceptor neuron axons to their synaptic targets in the brain via the P2 intermediate target neuron (PubMed:10892653). Involved in isoneural self-avoidance during dendrite arborization but not in heteroneural recognition and repulsion during tiling by related neurons of the same class (PubMed:17482551). Involved in regulating axon bifurcation and divergent extension in the developing mushroom body (PubMed:11856530, PubMed:15339648). Essential for axon arborisation in ellipsoid body (PubMed:11856530, PubMed:15339648). Exhibits an extraordinary level of molecular diversity resulting from alternative splicing (PubMed:10892653). Isoforms differing in their ectodomain makeup show a high degree of functional redundancy while isoforms with different transmembrane domains are involved in different neuronal morphogenetic processes and are differentially targeted to dendrites or axons (PubMed:15339648). The vast majority of isoforms exhibit strong isoform-specific homophilic binding (PubMed:15339666, PubMed:17889655). Individual cells express a distinct randomly generated repertoire of isoforms (PubMed:14758360). Cell surfaces bearing identical repertoires of Dscam1 isoforms, such as those from the same cell, trigger recognition and avoidance (PubMed:17482551). A subset of isoforms is expressed in fat body cells and hemocytes, cells that are part of the insect immune response, and these isoforms are secreted into the hemolymph (PubMed:16109846). The secreted form comprising the ectodomain can bind to bacteria, such as Escherichia coli, and may act as an opsonin enhancing their phagocytosis by hemocytes (PubMed:16109846).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

The Drosophila neural receptor Dscam1 (Down syndrome cell adhesion molecule 1) plays an essential role in neuronal wiring and self-avoidance. Dscam1 potentially encodes 19,008 ectodomains through alternative RNA splicing and exhibits exquisite isoform-specific homophilic binding, which makes it an exceptional example for studying protein binding specificity. However, structural information on Dscam1 is limited, which hinders illumination of the mechanism of Dscam1 isoform-specific recognition. Whether different Dscam1 isoforms adopt the same dimerization mode remains a subject of debate. We present 12 Dscam1 crystal structures, provide direct evidence indicating that all isoforms adopt a conserved homodimer geometry in a modular fashion, identify two mechanisms for the Ig2 binding domain to dispel electrostatic repulsion during dimerization, decode Ig2 binding specificity by a central motif at its symmetry center, uncover the role of glycosylation in Dscam1 homodimerization, and find electrostatic potential complementarity to help define the binding region and the antiparallel binding mode. We then propose a concept that the context of a protein may set restrictions to regulate its binding specificity, which provides a better understanding of protein recognition.

Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition.,Li SA, Cheng L, Yu Y, Chen Q Sci Adv. 2016 May 27;2(5):e1501118. doi: 10.1126/sciadv.1501118. eCollection 2016, May. PMID:27386517^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, Dixon JE, Zipursky SL. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell. 2000 Jun 9;101(6):671-84. PMID:10892653 doi:10.1016/s0092-8674(00)80878-8
↑ Wang J, Zugates CT, Liang IH, Lee CH, Lee T. Drosophila Dscam is required for divergent segregation of sister branches and suppresses ectopic bifurcation of axons. Neuron. 2002 Feb 14;33(4):559-71. PMID:11856530 doi:10.1016/s0896-6273(02)00570-6
↑ Neves G, Zucker J, Daly M, Chess A. Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat Genet. 2004 Mar;36(3):240-6. PMID:14758360 doi:10.1038/ng1299
↑ Wang J, Ma X, Yang JS, Zheng X, Zugates CT, Lee CH, Lee T. Transmembrane/juxtamembrane domain-dependent Dscam distribution and function during mushroom body neuronal morphogenesis. Neuron. 2004 Sep 2;43(5):663-72. PMID:15339648 doi:10.1016/j.neuron.2004.06.033
↑ Wojtowicz WM, Flanagan JJ, Millard SS, Zipursky SL, Clemens JC. Alternative splicing of Drosophila Dscam generates axon guidance receptors that exhibit isoform-specific homophilic binding. Cell. 2004 Sep 3;118(5):619-33. PMID:15339666 doi:10.1016/j.cell.2004.08.021
↑ Watson FL, Püttmann-Holgado R, Thomas F, Lamar DL, Hughes M, Kondo M, Rebel VI, Schmucker D. Extensive diversity of Ig-superfamily proteins in the immune system of insects. Science. 2005 Sep 16;309(5742):1874-8. PMID:16109846 doi:10.1126/science.1116887
↑ Matthews BJ, Kim ME, Flanagan JJ, Hattori D, Clemens JC, Zipursky SL, Grueber WB. Dendrite self-avoidance is controlled by Dscam. Cell. 2007 May 4;129(3):593-604. PMID:17482551 doi:10.1016/j.cell.2007.04.013
↑ Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL. A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell. 2007 Sep 21;130(6):1134-45. PMID:17889655 doi:10.1016/j.cell.2007.08.026
↑ Li SA, Cheng L, Yu Y, Chen Q. Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition. Sci Adv. 2016 May 27;2(5):e1501118. doi: 10.1126/sciadv.1501118. eCollection 2016, May. PMID:27386517 doi:http://dx.doi.org/10.1126/sciadv.1501118

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4xhq"

Categories: Drosophila melanogaster | Large Structures | Chen Q | Yu Y

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4xhq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XHQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.948&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xhq OCA], [https://pdbe.org/4xhq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xhq RCSB], [https://www.ebi.ac.uk/pdbsum/4xhq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xhq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/Q9NBA1_DROME Q9NBA1_DROME]
+[https://www.uniprot.org/uniprot/DSCA1_DROME DSCA1_DROME] Cell surface receptor involved in guidance and targeting of growing nerve axons (PubMed:10892653). Required during Bolwig's organ differentiation for accurate and efficient targeting of photoreceptor neuron axons to their synaptic targets in the brain via the P2 intermediate target neuron (PubMed:10892653). Involved in isoneural self-avoidance during dendrite arborization but not in heteroneural recognition and repulsion during tiling by related neurons of the same class (PubMed:17482551). Involved in regulating axon bifurcation and divergent extension in the developing mushroom body (PubMed:11856530, PubMed:15339648). Essential for axon arborisation in ellipsoid body (PubMed:11856530, PubMed:15339648). Exhibits an extraordinary level of molecular diversity resulting from alternative splicing (PubMed:10892653). Isoforms differing in their ectodomain makeup show a high degree of functional redundancy while isoforms with different transmembrane domains are involved in different neuronal morphogenetic processes and are differentially targeted to dendrites or axons (PubMed:15339648). The vast majority of isoforms exhibit strong isoform-specific homophilic binding (PubMed:15339666, PubMed:17889655). Individual cells express a distinct randomly generated repertoire of isoforms (PubMed:14758360). Cell surfaces bearing identical repertoires of Dscam1 isoforms, such as those from the same cell, trigger recognition and avoidance (PubMed:17482551). A subset of isoforms is expressed in fat body cells and hemocytes, cells that are part of the insect immune response, and these isoforms are secreted into the hemolymph (PubMed:16109846). The secreted form comprising the ectodomain can bind to bacteria, such as Escherichia coli, and may act as an opsonin enhancing their phagocytosis by hemocytes (PubMed:16109846).<ref>PMID:10892653</ref> <ref>PMID:11856530</ref> <ref>PMID:14758360</ref> <ref>PMID:15339648</ref> <ref>PMID:15339666</ref> <ref>PMID:16109846</ref> <ref>PMID:17482551</ref> <ref>PMID:17889655</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4xhq

From Proteopedia

Current revision

Re-refinement the crystal structure of Dscam1 isoform 1.34, N-terminal four Ig domains

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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