3ewe: Difference between revisions

Latest revision as of 07:57, 9 October 2024

Crystal Structure of the Nup85/Seh1 Complex

Structural highlights

3ewe is a 4 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 3.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUP85_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. NUP85 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eight-fold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the Nup85*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 A resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identify interactions that define the organization of the Nup84 complex based on comparison with vesicle coats and confirmed the sites by mutagenesis. We propose the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice providing docking sites for additional nucleoporins.

Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats.,Brohawn SG, Leksa NC, Spear ED, Rajashankar KR, Schwartz TU Science. 2008 Oct 30. PMID:18974315^[7]

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

References

↑ Goldstein AL, Snay CA, Heath CV, Cole CN. Pleiotropic nuclear defects associated with a conditional allele of the novel nucleoporin Rat9p/Nup85p. Mol Biol Cell. 1996 Jun;7(6):917-34. PMID:8816998
↑ Santos-Rosa H, Moreno H, Simos G, Segref A, Fahrenkrog B, Pante N, Hurt E. Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol Cell Biol. 1998 Nov;18(11):6826-38. PMID:9774696
↑ Stage-Zimmermann T, Schmidt U, Silver PA. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell. 2000 Nov;11(11):3777-89. PMID:11071906
↑ Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec;1(12):930-46. PMID:12543930
↑ 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
↑ 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
↑ Brohawn SG, Leksa NC, Spear ED, Rajashankar KR, Schwartz TU. Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats. Science. 2008 Oct 30. PMID:18974315

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Goldstein AL, Snay CA, Heath CV, Cole CN. Pleiotropic nuclear defects associated with a conditional allele of the novel nucleoporin Rat9p/Nup85p. Mol Biol Cell. 1996 Jun;7(6):917-34. PMID:8816998

[2] Santos-Rosa H, Moreno H, Simos G, Segref A, Fahrenkrog B, Pante N, Hurt E. Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol Cell Biol. 1998 Nov;18(11):6826-38. PMID:9774696

[3] Stage-Zimmermann T, Schmidt U, Silver PA. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell. 2000 Nov;11(11):3777-89. PMID:11071906

[4] Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec;1(12):930-46. PMID:12543930

[5] 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

[6] 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

[7] Brohawn SG, Leksa NC, Spear ED, Rajashankar KR, Schwartz TU. Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats. Science. 2008 Oct 30. PMID:18974315

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[2]

[3]

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[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='3ewe' size='340' side='right'caption='[[3ewe]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ewe]] is a 4 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=3EWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EWE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ewe]] is a 4 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=3EWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EWE FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SEH1, YGL100W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), J1624, NUP85, RAT9, YJR042W ([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]] 3.5&#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=3ewe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ewe OCA], [https://pdbe.org/3ewe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ewe RCSB], [https://www.ebi.ac.uk/pdbsum/3ewe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ewe ProSAT]</span></td></tr>
 </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>  [[https://www.uniprot.org/uniprot/NUP85_YEAST NUP85_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. NUP85 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.<ref>PMID:8816998</ref> <ref>PMID:9774696</ref> <ref>PMID:11071906</ref> <ref>PMID:12543930</ref> <ref>PMID:11823431</ref> <ref>PMID:12730220</ref>
+[https://www.uniprot.org/uniprot/NUP85_YEAST NUP85_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. NUP85 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.<ref>PMID:8816998</ref> <ref>PMID:9774696</ref> <ref>PMID:11071906</ref> <ref>PMID:12543930</ref> <ref>PMID:11823431</ref> <ref>PMID:12730220</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 14: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ew/3ewe_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 35: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Brohawn, S G]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Leksa, N C]]
+[[Category: Brohawn SG]]
-[[Category: Rajashankar, K R]]
+[[Category: Leksa NC]]
-[[Category: Schwartz, T U]]
+[[Category: Rajashankar KR]]
-[[Category: Cell membrane]]
+[[Category: Schwartz TU]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Mrna transport]]
-[[Category: Nuclear pore complex]]
-[[Category: Nucleoporin]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protein transport]]
-[[Category: Structural protein]]
-[[Category: Translocation]]
-[[Category: Transport]]
-[[Category: Wd repeat]]

3ewe: Difference between revisions

Latest revision as of 07:57, 9 October 2024

Crystal Structure of the Nup85/Seh1 Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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