6b4e: Difference between revisions

Latest revision as of 14:32, 4 October 2023

Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex

Structural highlights

6b4e is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	EDO, PRO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLE1_YEAST Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1*Nxt1 from mRNAs. Here, we report crystal structures of Gle1*Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1*Nup42*DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans.

Structural and functional analysis of mRNA export regulation by the nuclear pore complex.,Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A Nat Commun. 2018 Jun 13;9(1):2319. doi: 10.1038/s41467-018-04459-3. PMID:29899397^[6]

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

References

↑ Hodge CA, Colot HV, Stafford P, Cole CN. Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. EMBO J. 1999 Oct 15;18(20):5778-88. PMID:10523319 doi:10.1093/emboj/18.20.5778
↑ Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, Stutz F. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J. 1999 Oct 15;18(20):5761-77. PMID:10610322 doi:10.1093/emboj/18.20.5761
↑ Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000 Feb 21;148(4):635-51. PMID:10684247
↑ Jensen TH, Patricio K, McCarthy T, Rosbash M. A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell. 2001 Apr;7(4):887-98. PMID:11336711
↑ Suntharalingam M, Alcazar-Roman AR, Wente SR. Nuclear export of the yeast mRNA-binding protein Nab2 is linked to a direct interaction with Gfd1 and to Gle1 function. J Biol Chem. 2004 Aug 20;279(34):35384-91. Epub 2004 Jun 18. PMID:15208322 doi:10.1074/jbc.M402044200
↑ Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun. 2018 Jun 13;9(1):2319. doi: 10.1038/s41467-018-04459-3. PMID:29899397 doi:https://dx.doi.org/10.1038/s41467-018-04459-3

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hodge CA, Colot HV, Stafford P, Cole CN. Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. EMBO J. 1999 Oct 15;18(20):5778-88. PMID:10523319 doi:10.1093/emboj/18.20.5778

[2] Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, Stutz F. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J. 1999 Oct 15;18(20):5761-77. PMID:10610322 doi:10.1093/emboj/18.20.5761

[3] Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000 Feb 21;148(4):635-51. PMID:10684247

[4] Jensen TH, Patricio K, McCarthy T, Rosbash M. A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell. 2001 Apr;7(4):887-98. PMID:11336711

[5] Suntharalingam M, Alcazar-Roman AR, Wente SR. Nuclear export of the yeast mRNA-binding protein Nab2 is linked to a direct interaction with Gfd1 and to Gle1 function. J Biol Chem. 2004 Aug 20;279(34):35384-91. Epub 2004 Jun 18. PMID:15208322 doi:10.1074/jbc.M402044200

[6] Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun. 2018 Jun 13;9(1):2319. doi: 10.1038/s41467-018-04459-3. PMID:29899397 doi:https://dx.doi.org/10.1038/s41467-018-04459-3

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='6b4e' size='340' side='right'caption='[[6b4e]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6b4e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B4E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</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]] 1.75&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLE1, BRR3, RSS1, YDL207W, D1049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), NUP42, RIP1, UIP1, YDR192C, YD9346.04C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [http://pdbe.org/6b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [http://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></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=6b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b4e OCA], [https://pdbe.org/6b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b4e RCSB], [https://www.ebi.ac.uk/pdbsum/6b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b4e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref>  [[http://www.uniprot.org/uniprot/NUP42_YEAST NUP42_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP42 is specifically important for nuclear protein and mRNA export.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10805742</ref> <ref>PMID:10952996</ref> <ref>PMID:11387327</ref> <ref>PMID:12604785</ref> <ref>PMID:12917401</ref> <ref>PMID:15039779</ref>
+[https://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Cai, S W]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Correia, A R]]
+[[Category: Cai SW]]
-[[Category: Hoelz, A]]
+[[Category: Correia AR]]
-[[Category: Huber, F M]]
+[[Category: Hoelz A]]
-[[Category: Jette, C A]]
+[[Category: Huber FM]]
-[[Category: Lin, D H]]
+[[Category: Jette CA]]
-[[Category: Complex]]
+[[Category: Lin DH]]
-[[Category: Dead-box helicase]]
-[[Category: Mrna export]]
-[[Category: Nuclear pore complex]]
-[[Category: Transport protein]]

6b4e: Difference between revisions

Latest revision as of 14:32, 4 October 2023

Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools