3f3p

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212

Structural highlights

3f3p is a 12 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 3.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SEH1_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. Involved in nuclear poly(A)+ RNA export and NPC biogenesis. It is also required for normal nuclear morphology. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

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

Publication Abstract from PubMed

We recently proposed a cylindrical coat for the nuclear pore membrane in the nuclear pore complex (NPC). This scaffold is generated by multiple copies of seven nucleoporins. Here, we report three crystal structures of the nucleoporin pair Seh1*Nup85, which is part of the coat cylinder. The Seh1*Nup85 assembly bears resemblance in its shape and dimensions to that of another nucleoporin pair, Sec13*Nup145C. Furthermore, the Seh1*Nup85 structures reveal a hinge motion that may facilitate conformational changes in the NPC during import of integral membrane proteins and/or during nucleocytoplasmic transport. We propose that Seh1*Nup85 and Sec13*Nup145C form 16 alternating, vertical rods that are horizontally linked by the three remaining nucleoporins of the coat cylinder. Shared architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and support the notion that the NPC coat represents another class of membrane coats.

A fence-like coat for the nuclear pore membrane.,Debler EW, Ma Y, Seo HS, Hsia KC, Noriega TR, Blobel G, Hoelz A Mol Cell. 2008 Dec 26;32(6):815-26. PMID:19111661^[5]

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

References

↑ Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell. 1996 Jan 26;84(2):265-75. PMID:8565072
↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
↑ Teixeira MT, Dujon B, Fabre E. Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae. J Mol Biol. 2002 Aug 23;321(4):551-61. PMID:12206772
↑ Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics. 2011 Jun;10(6):M110.006478. doi: 10.1074/mcp.M110.006478., Epub 2011 Mar 31. PMID:21454883 doi:10.1074/mcp.M110.006478
↑ Debler EW, Ma Y, Seo HS, Hsia KC, Noriega TR, Blobel G, Hoelz A. A fence-like coat for the nuclear pore membrane. Mol Cell. 2008 Dec 26;32(6):815-26. PMID:19111661 doi:http://dx.doi.org/10.1016/j.molcel.2008.12.001

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f3p"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212==
-<StructureSection load='3f3p' size='340' side='right' caption='[[3f3p]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='3f3p' size='340' side='right'caption='[[3f3p]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f3p]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F3P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f3p]] is a 12 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=3F3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F3P FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 3.2&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f3f|3f3f]], [[3f3g|3f3g]]</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></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SEH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), NUP85, RAT9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3f3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f3p OCA], [https://pdbe.org/3f3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f3p RCSB], [https://www.ebi.ac.uk/pdbsum/3f3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f3p ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3f3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f3p RCSB], [http://www.ebi.ac.uk/pdbsum/3f3p PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/SEH1_YEAST SEH1_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. Involved in nuclear poly(A)+ RNA export and NPC biogenesis. It is also required for normal nuclear morphology. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.<ref>PMID:8565072</ref> <ref>PMID:11823431</ref> <ref>PMID:12206772</ref> <ref>PMID:21454883</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/3f3p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/3f3p_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3f3p ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3f3p" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nucleoporin|Nucleoporin]]
+*[[Nucleoporin 3D structures|Nucleoporin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Blobel, G.]]
+[[Category: Blobel G]]
-[[Category: Debler, E W.]]
+[[Category: Debler EW]]
-[[Category: Hoelz, A.]]
+[[Category: Hoelz A]]
-[[Category: Hseo, H.]]
+[[Category: Hseo H]]
-[[Category: Ma, Y.]]
+[[Category: Ma Y]]
-[[Category: Beta-propeller]]
-[[Category: Macromolecular assembly]]
-[[Category: Membrane coat]]
-[[Category: Mrna transport]]
-[[Category: Nuclear pore complex]]
-[[Category: Nucleocytoplasmic transport]]
-[[Category: Nucleoporin]]
-[[Category: Nucleoporin complex]]
-[[Category: Nucleus]]
-[[Category: Protein complex]]
-[[Category: Protein transport]]
-[[Category: Solenoid domain]]
-[[Category: Structural protein]]
-[[Category: Translocation]]
-[[Category: Wd repeat]]

3f3p

From Proteopedia

Current revision

Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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