6ixe: Difference between revisions

Latest revision as of 11:07, 30 October 2024

Crystal structure of SeMet apo SH3BP5 (I41)

Structural highlights

6ixe 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 3.35Å
Ligands:	MSE, SIN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

3BP5_HUMAN Inhibits the auto- and transphosphorylation activity of BTK. Plays a negative regulatory role in BTK-related cytoplasmic signaling in B-cells. May be involved in BCR-induced apoptotic cell death.^[1] ^[2]

Publication Abstract from PubMed

The Rab GTPase family is a major regulator of membrane traffic in eukaryotic cells. The Rab11 subfamily plays important roles in specific trafficking events such as exocytosis, endosomal recycling, and cytokinesis. SH3BP5 and SH3BP5-like (SH3BP5L) proteins have recently been found to serve as guanine nucleotide exchange factors (GEF) for Rab11. Here, we report the crystal structures of the SH3BP5 GEF domain alone and its complex with Rab11a. SH3BP5 exhibits a V-shaped structure comprising two coiled coils. The coiled coil composed of alpha1, and alpha4 is solely responsible for the Rab11a binding and GEF activity. SH3BP5 pulls out and deforms switch I of Rab11a so as to facilitate the GDP release from Rab11a. SH3BP5 interacts with the N-terminal region, switch I, interswitch, and switch II of Rab11a. SH3BP5 and SH3BP5L localize to Rab11-positive recycling endosomes and show GEF activity for all of the Rab11 family but not for Rab14. Fluorescence-based GEF assays combined with site-directed mutagenesis reveal the essential interactions between SH3BP5 and Rab11 family proteins for the GEF reaction on recycling endosomes.

Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.,Goto-Ito S, Morooka N, Yamagata A, Sato Y, Sato K, Fukai S Life Sci Alliance. 2019 Mar 14;2(2). pii: 2/2/e201900297. doi:, 10.26508/lsa.201900297. Print 2019 Apr. PMID:30872413^[3]

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

References

↑ Yamadori T, Baba Y, Matsushita M, Hashimoto S, Kurosaki M, Kurosaki T, Kishimoto T, Tsukada S. Bruton's tyrosine kinase activity is negatively regulated by Sab, the Btk-SH3 domain-binding protein. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6341-6. PMID:10339589
↑ Matsushita M, Yamadori T, Kato S, Takemoto Y, Inazawa J, Baba Y, Hashimoto S, Sekine S, Arai S, Kunikata T, Kurimoto M, Kishimoto T, Tsukada S. Identification and characterization of a novel SH3-domain binding protein, Sab, which preferentially associates with Bruton's tyrosine kinase (BtK). Biochem Biophys Res Commun. 1998 Apr 17;245(2):337-43. PMID:9571151 doi:https://dx.doi.org/10.1006/bbrc.1998.8420
↑ Goto-Ito S, Morooka N, Yamagata A, Sato Y, Sato K, Fukai S. Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance. 2019 Mar 14;2(2). pii: 2/2/e201900297. doi:, 10.26508/lsa.201900297. Print 2019 Apr. PMID:30872413 doi:https://dx.doi.org/10.26508/lsa.201900297

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OCA

[1] Yamadori T, Baba Y, Matsushita M, Hashimoto S, Kurosaki M, Kurosaki T, Kishimoto T, Tsukada S. Bruton's tyrosine kinase activity is negatively regulated by Sab, the Btk-SH3 domain-binding protein. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6341-6. PMID:10339589

[2] Matsushita M, Yamadori T, Kato S, Takemoto Y, Inazawa J, Baba Y, Hashimoto S, Sekine S, Arai S, Kunikata T, Kurimoto M, Kishimoto T, Tsukada S. Identification and characterization of a novel SH3-domain binding protein, Sab, which preferentially associates with Bruton's tyrosine kinase (BtK). Biochem Biophys Res Commun. 1998 Apr 17;245(2):337-43. PMID:9571151 doi:https://dx.doi.org/10.1006/bbrc.1998.8420

[3] Goto-Ito S, Morooka N, Yamagata A, Sato Y, Sato K, Fukai S. Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance. 2019 Mar 14;2(2). pii: 2/2/e201900297. doi:, 10.26508/lsa.201900297. Print 2019 Apr. PMID:30872413 doi:https://dx.doi.org/10.26508/lsa.201900297

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6ixe' size='340' side='right'caption='[[6ixe]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ixe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IXE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ixe]] 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=6IXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IXE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 3.35&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SH3BP5, SAB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ixe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ixe OCA], [https://pdbe.org/6ixe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ixe RCSB], [https://www.ebi.ac.uk/pdbsum/6ixe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ixe ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ixe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ixe OCA], [http://pdbe.org/6ixe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ixe RCSB], [http://www.ebi.ac.uk/pdbsum/6ixe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ixe ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/3BP5_HUMAN 3BP5_HUMAN]] Inhibits the auto- and transphosphorylation activity of BTK. Plays a negative regulatory role in BTK-related cytoplasmic signaling in B-cells. May be involved in BCR-induced apoptotic cell death.<ref>PMID:10339589</ref> <ref>PMID:9571151</ref>
+[https://www.uniprot.org/uniprot/3BP5_HUMAN 3BP5_HUMAN] Inhibits the auto- and transphosphorylation activity of BTK. Plays a negative regulatory role in BTK-related cytoplasmic signaling in B-cells. May be involved in BCR-induced apoptotic cell death.<ref>PMID:10339589</ref> <ref>PMID:9571151</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Fukai, S]]
+[[Category: Fukai S]]
-[[Category: Goto-Ito, S]]
+[[Category: Goto-Ito S]]
-[[Category: Sato, Y]]
+[[Category: Sato Y]]
-[[Category: Yamagata, A]]
+[[Category: Yamagata A]]
-[[Category: Gef]]
-[[Category: Rab11]]
-[[Category: Sh3bp5]]
-[[Category: Signaling protein]]

6ixe: Difference between revisions

Latest revision as of 11:07, 30 October 2024

Crystal structure of SeMet apo SH3BP5 (I41)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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