2rfo: Difference between revisions

Latest revision as of 13:54, 13 March 2024

Crystral Structure of the nucleoporin Nic96

Structural highlights

2rfo is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIC96_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. NIC96, which is localized to the core of the NPC and the distal ring of the nuclear basket, is required for de novo assembly of NPCs. It is involved in nuclear GSP1 import.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Grandi P, Schlaich N, Tekotte H, Hurt EC. Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p. EMBO J. 1995 Jan 3;14(1):76-87. PMID:7828598
↑ Nehrbass U, Rout MP, Maguire S, Blobel G, Wozniak RW. The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex. J Cell Biol. 1996 Jun;133(6):1153-62. PMID:8682855
↑ Schlaich NL, Haner M, Lustig A, Aebi U, Hurt EC. In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p. Mol Biol Cell. 1997 Jan;8(1):33-46. PMID:9017593
↑ Kosova B, Pante N, Rollenhagen C, Hurt E. Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane. J Biol Chem. 1999 Aug 6;274(32):22646-51. PMID:10428845
↑ Kosova B, Pante N, Rollenhagen C, Podtelejnikov A, Mann M, Aebi U, Hurt E. Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p. J Biol Chem. 2000 Jan 7;275(1):343-50. PMID:10617624
↑ Gomez-Ospina N, Morgan G, Giddings TH Jr, Kosova B, Hurt E, Winey M. Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction. J Struct Biol. 2000 Oct;132(1):1-5. PMID:11121302 doi:10.1006/jsbi.2000.4305
↑ Fahrenkrog B, Aris JP, Hurt EC, Pante N, Aebi U. Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy. J Struct Biol. 2000 Apr;129(2-3):295-305. PMID:10806080 doi:https://dx.doi.org/10.1006/jsbi.2000.4223
↑ Bailer SM, Balduf C, Hurt E. The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport. Mol Cell Biol. 2001 Dec;21(23):7944-55. PMID:11689687 doi:https://dx.doi.org/10.1128/MCB.21.23.7944-7955.2001
↑ Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW. Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes. J Cell Biol. 2002 Oct 28;159(2):267-78. Epub 2002 Oct 28. PMID:12403813 doi:10.1083/jcb.200203079
↑ Damelin M, Silver PA. In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophys J. 2002 Dec;83(6):3626-36. PMID:12496130 doi:https://dx.doi.org/S0006-3495(02)75363-0
↑ Gao H, Sumanaweera N, Bailer SM, Stochaj U. Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p. J Biol Chem. 2003 Jul 11;278(28):25331-40. Epub 2003 May 1. PMID:12730220 doi:https://dx.doi.org/10.1074/jbc.M301607200

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OCA

[1] Grandi P, Schlaich N, Tekotte H, Hurt EC. Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p. EMBO J. 1995 Jan 3;14(1):76-87. PMID:7828598

[2] Nehrbass U, Rout MP, Maguire S, Blobel G, Wozniak RW. The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex. J Cell Biol. 1996 Jun;133(6):1153-62. PMID:8682855

[3] Schlaich NL, Haner M, Lustig A, Aebi U, Hurt EC. In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p. Mol Biol Cell. 1997 Jan;8(1):33-46. PMID:9017593

[4] Kosova B, Pante N, Rollenhagen C, Hurt E. Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane. J Biol Chem. 1999 Aug 6;274(32):22646-51. PMID:10428845

[5] Kosova B, Pante N, Rollenhagen C, Podtelejnikov A, Mann M, Aebi U, Hurt E. Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p. J Biol Chem. 2000 Jan 7;275(1):343-50. PMID:10617624

[6] Gomez-Ospina N, Morgan G, Giddings TH Jr, Kosova B, Hurt E, Winey M. Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction. J Struct Biol. 2000 Oct;132(1):1-5. PMID:11121302 doi:10.1006/jsbi.2000.4305

[7] Fahrenkrog B, Aris JP, Hurt EC, Pante N, Aebi U. Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy. J Struct Biol. 2000 Apr;129(2-3):295-305. PMID:10806080 doi:https://dx.doi.org/10.1006/jsbi.2000.4223

[8] Bailer SM, Balduf C, Hurt E. The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport. Mol Cell Biol. 2001 Dec;21(23):7944-55. PMID:11689687 doi:https://dx.doi.org/10.1128/MCB.21.23.7944-7955.2001

[9] Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW. Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes. J Cell Biol. 2002 Oct 28;159(2):267-78. Epub 2002 Oct 28. PMID:12403813 doi:10.1083/jcb.200203079

[10] Damelin M, Silver PA. In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophys J. 2002 Dec;83(6):3626-36. PMID:12496130 doi:https://dx.doi.org/S0006-3495(02)75363-0

[11] Gao H, Sumanaweera N, Bailer SM, Stochaj U. Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p. J Biol Chem. 2003 Jul 11;278(28):25331-40. Epub 2003 May 1. PMID:12730220 doi:https://dx.doi.org/10.1074/jbc.M301607200

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

[9]

[10]

[11]

@@ Line 3: / Line 3: @@
 <StructureSection load='2rfo' size='340' side='right'caption='[[2rfo]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rfo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RFO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rfo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RFO FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NIC96 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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]] 2.6&#8491;</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=2rfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rfo OCA], [https://pdbe.org/2rfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rfo RCSB], [https://www.ebi.ac.uk/pdbsum/2rfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rfo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NIC96_YEAST NIC96_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. NIC96, which is localized to the core of the NPC and the distal ring of the nuclear basket, is required for de novo assembly of NPCs. It is involved in nuclear GSP1 import.<ref>PMID:7828598</ref> <ref>PMID:8682855</ref> <ref>PMID:9017593</ref> <ref>PMID:10428845</ref> <ref>PMID:10617624</ref> <ref>PMID:11121302</ref> <ref>PMID:10806080</ref> <ref>PMID:11689687</ref> <ref>PMID:12403813</ref> <ref>PMID:12496130</ref> <ref>PMID:12730220</ref>
+[https://www.uniprot.org/uniprot/NIC96_YEAST NIC96_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. NIC96, which is localized to the core of the NPC and the distal ring of the nuclear basket, is required for de novo assembly of NPCs. It is involved in nuclear GSP1 import.<ref>PMID:7828598</ref> <ref>PMID:8682855</ref> <ref>PMID:9017593</ref> <ref>PMID:10428845</ref> <ref>PMID:10617624</ref> <ref>PMID:11121302</ref> <ref>PMID:10806080</ref> <ref>PMID:11689687</ref> <ref>PMID:12403813</ref> <ref>PMID:12496130</ref> <ref>PMID:12730220</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rfo ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Nic96 is a conserved nucleoporin that recruits the Nsp1-Nup49-Nup57 complex, a module with Phe-Gly (FG) repeats, to the central transport channel of the nuclear pore complex (NPC). Nic96 binds the Nsp1 complex via its N domain and assembles into the NPC framework via its central and C domain. Here, we report the crystal structure of a large structural nucleoporin, Nic96 without its N domain (Nic96DeltaN). Nic96DeltaN is composed of three domains and is a straight molecule that--although almost entirely helical--exhibits strong deviations from the predicted alpha-solenoid fold. The missing N domain projects midway from the Nic96 molecule, indicating how the Nsp1 complex might be located with respect to the rod-like Nic96. Notably, Nic96DeltaN binds in vitro to FG repeats of the Nsp1 complex. These data suggest a model of how Nic96 could organize a transport module with coiled-coil domains and FG repeats in the central pore channel.
-Structural basis of the nic96 subcomplex organization in the nuclear pore channel.,Schrader N, Stelter P, Flemming D, Kunze R, Hurt E, Vetter IR Mol Cell. 2008 Jan 18;29(1):46-55. PMID:18206968<ref>PMID:18206968</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2rfo" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Flemming, D]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Hurt, E]]
+[[Category: Flemming D]]
-[[Category: Kunze, K]]
+[[Category: Hurt E]]
-[[Category: Schrader, N]]
+[[Category: Kunze K]]
-[[Category: Stelter, P]]
+[[Category: Schrader N]]
-[[Category: Vetter, I R]]
+[[Category: Stelter P]]
-[[Category: Alpha-alpha-superhelix]]
+[[Category: Vetter IR]]
-[[Category: Mrna transport]]
-[[Category: Nuclear pore complex]]
-[[Category: Nucleus]]
-[[Category: Protein transport]]
-[[Category: Structural protein]]
-[[Category: Translocation]]
-[[Category: Transport]]

2rfo: Difference between revisions

Latest revision as of 13:54, 13 March 2024

Crystral Structure of the nucleoporin Nic96

Structural highlights

Function

Evolutionary Conservation

See Also

References

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