6zr7

From Proteopedia

(Difference between revisions)

Revision as of 11:56, 1 February 2024

X-ray structure of human Dscam Ig7-Ig9

Structural highlights

6zr7 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DSCAM_HUMAN Cell adhesion molecule that plays a role in neuronal self-avoidance. Promotes repulsion between specific neuronal processes of either the same cell or the same subtype of cells. Mediates within retinal amacrine and ganglion cell subtypes both isoneuronal self-avoidance for creating an orderly dendritic arborization and heteroneuronal self-avoidance to maintain the mosaic spacing between amacrine and ganglion cell bodies (PubMed:10925149). Receptor for netrin required for axon guidance independently of and in collaboration with the receptor DCC. Might also collaborate with UNC5C in NTN1-mediated axon repulsion independently of DCC (By similarity). In spinal cord development plays a role in guiding commissural axons projection and pathfinding across the ventral midline to reach the floor plate upon ligand binding (PubMed:18585357, PubMed:19196994). Mediates intracellular signaling by stimulating the activation of MAPK8 and MAP kinase p38 (PubMed:18585357, PubMed:19196994). Adhesion molecule that promotes lamina-specific synaptic connections in the retina: expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions (By similarity).[UniProtKB:F1NY98][UniProtKB:Q9ERC8]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy.

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.,Kozak S, Bloch Y, De Munck S, Mikula A, Bento I, Savvides SN, Meijers R Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1244-1255. doi:, 10.1107/S2059798320013753. Epub 2020 Nov 24. PMID:33263330^[4]

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

References

↑ Agarwala KL, Nakamura S, Tsutsumi Y, Yamakawa K. Down syndrome cell adhesion molecule DSCAM mediates homophilic intercellular adhesion. Brain Res Mol Brain Res. 2000 Jun 23;79(1-2):118-26. PMID:10925149 doi:10.1016/s0169-328x(00)00108-x
↑ Ly A, Nikolaev A, Suresh G, Zheng Y, Tessier-Lavigne M, Stein E. DSCAM is a netrin receptor that collaborates with DCC in mediating turning responses to netrin-1. Cell. 2008 Jun 27;133(7):1241-54. PMID:18585357 doi:10.1016/j.cell.2008.05.030
↑ Liu G, Li W, Wang L, Kar A, Guan KL, Rao Y, Wu JY. DSCAM functions as a netrin receptor in commissural axon pathfinding. Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2951-6. PMID:19196994 doi:10.1073/pnas.0811083106
↑ Kozak S, Bloch Y, De Munck S, Mikula A, Bento I, Savvides SN, Meijers R. Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis. Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1244-1255. doi:, 10.1107/S2059798320013753. Epub 2020 Nov 24. PMID:33263330 doi:http://dx.doi.org/10.1107/S2059798320013753

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/6zr7"

Categories: Homo sapiens | Large Structures | Bento I | Kozak S | Meijers R

@@ Line 1: / Line 1: @@
 ==X-ray structure of human Dscam Ig7-Ig9==
-<StructureSection load='6zr7' size='340' side='right'caption='[[6zr7]]' scene=''>
+<StructureSection load='6zr7' size='340' side='right'caption='[[6zr7]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZR7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZR7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6zr7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZR7 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zr7 OCA], [http://pdbe.org/6zr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zr7 RCSB], [http://www.ebi.ac.uk/pdbsum/6zr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zr7 ProSAT]</span></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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900067:3-sialyl-N-acetyllactosamine'>PRD_900067</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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=6zr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zr7 OCA], [https://pdbe.org/6zr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zr7 RCSB], [https://www.ebi.ac.uk/pdbsum/6zr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zr7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DSCAM_HUMAN DSCAM_HUMAN] Cell adhesion molecule that plays a role in neuronal self-avoidance. Promotes repulsion between specific neuronal processes of either the same cell or the same subtype of cells. Mediates within retinal amacrine and ganglion cell subtypes both isoneuronal self-avoidance for creating an orderly dendritic arborization and heteroneuronal self-avoidance to maintain the mosaic spacing between amacrine and ganglion cell bodies (PubMed:10925149). Receptor for netrin required for axon guidance independently of and in collaboration with the receptor DCC. Might also collaborate with UNC5C in NTN1-mediated axon repulsion independently of DCC (By similarity). In spinal cord development plays a role in guiding commissural axons projection and pathfinding across the ventral midline to reach the floor plate upon ligand binding (PubMed:18585357, PubMed:19196994). Mediates intracellular signaling by stimulating the activation of MAPK8 and MAP kinase p38 (PubMed:18585357, PubMed:19196994). Adhesion molecule that promotes lamina-specific synaptic connections in the retina: expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions (By similarity).[UniProtKB:F1NY98][UniProtKB:Q9ERC8]<ref>PMID:10925149</ref> <ref>PMID:18585357</ref> <ref>PMID:19196994</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy.
+Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.,Kozak S, Bloch Y, De Munck S, Mikula A, Bento I, Savvides SN, Meijers R Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1244-1255. doi:, 10.1107/S2059798320013753. Epub 2020 Nov 24. PMID:33263330<ref>PMID:33263330</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6zr7" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
 [[Category: Bento I]]
 [[Category: Kozak S]]
 [[Category: Meijers R]]

6zr7

From Proteopedia

Revision as of 11:56, 1 February 2024

X-ray structure of human Dscam Ig7-Ig9

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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