3kfo

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae

Structural highlights

3kfo is a 1 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 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NU133_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. NUP133 is involved in nuclear poly(A)+ RNA, tRNA 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] ^[7]

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), responsible for the nucleo-cytoplasmic exchange of proteins and nucleic acids, are dynamic macromolecular assemblies forming an eight-fold symmetric co-axial ring structure. Yeast (Saccharomyces cerevisiae) NPCs are made up of at least 456 polypeptide chains of ~30 distinct sequences. Many of these components (nucleoporins, Nups) share similar structural motifs and form stable subcomplexes. We have determined a high-resolution crystal structure of the C-terminal domain of yeast Nup133 (ScNup133), a component of the heptameric Nup84 subcomplex. Expression tests yielded ScNup133(944-1157) that produced crystals diffracting to 1.9A resolution. ScNup133(944-1157) adopts essentially an all alpha-helical fold, with a short two stranded beta-sheet at the C-terminus. The 11 alpha-helices of ScNup133(944-1157) form a compact fold. In contrast, the previously determined structure of human Nup133(934-1156) bound to a fragment of human Nup107 has its constituent alpha-helices are arranged in two globular blocks. These differences may reflect structural divergence among homologous nucleoporins.

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.,Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. PMID:21365675^[8]

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

References

↑ Doye V, Wepf R, Hurt EC. A novel nuclear pore protein Nup133p with distinct roles in poly(A)+ RNA transport and nuclear pore distribution. EMBO J. 1994 Dec 15;13(24):6062-75. PMID:7813444
↑ Pemberton LF, Rout MP, Blobel G. Disruption of the nucleoporin gene NUP133 results in clustering of nuclear pore complexes. Proc Natl Acad Sci U S A. 1995 Feb 14;92(4):1187-91. PMID:7862658
↑ Sharma K, Fabre E, Tekotte H, Hurt EC, Tollervey D. Yeast nucleoporin mutants are defective in pre-tRNA splicing. Mol Cell Biol. 1996 Jan;16(1):294-301. PMID:8524308
↑ Belgareh N, Doye V. Dynamics of nuclear pore distribution in nucleoporin mutant yeast cells. J Cell Biol. 1997 Feb 24;136(4):747-59. PMID:9049242
↑ 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
↑ 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:http://dx.doi.org/10.1074/jbc.M301607200
↑ Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins. 2011 Jan 4. doi: 10.1002/prot.22973. PMID:21365675 doi:10.1002/prot.22973

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/3kfo"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae==
-<StructureSection load='3kfo' size='340' side='right' caption='[[3kfo]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='3kfo' size='340' side='right'caption='[[3kfo]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kfo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KFO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kfo]] is a 1 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=3KFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KFO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.9&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUP133, RAT3, YKR082W, YKR402 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3kfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kfo OCA], [https://pdbe.org/3kfo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kfo RCSB], [https://www.ebi.ac.uk/pdbsum/3kfo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kfo 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=3kfo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kfo OCA], [http://pdbe.org/3kfo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kfo RCSB], [http://www.ebi.ac.uk/pdbsum/3kfo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kfo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NU133_YEAST NU133_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. NUP133 is involved in nuclear poly(A)+ RNA, tRNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.<ref>PMID:7813444</ref> <ref>PMID:7862658</ref> <ref>PMID:8524308</ref> <ref>PMID:9049242</ref> <ref>PMID:11071906</ref> <ref>PMID:11823431</ref> <ref>PMID:12730220</ref>
+[https://www.uniprot.org/uniprot/NU133_YEAST NU133_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. NUP133 is involved in nuclear poly(A)+ RNA, tRNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.<ref>PMID:7813444</ref> <ref>PMID:7862658</ref> <ref>PMID:8524308</ref> <ref>PMID:9049242</ref> <ref>PMID:11071906</ref> <ref>PMID:11823431</ref> <ref>PMID:12730220</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/kf/3kfo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/3kfo_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>
 </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=3kfo ConSurf].
 <div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nuclear pore complexes (NPCs), responsible for the nucleo-cytoplasmic exchange of proteins and nucleic acids, are dynamic macromolecular assemblies forming an eight-fold symmetric co-axial ring structure. Yeast (Saccharomyces cerevisiae) NPCs are made up of at least 456 polypeptide chains of ~30 distinct sequences. Many of these components (nucleoporins, Nups) share similar structural motifs and form stable subcomplexes. We have determined a high-resolution crystal structure of the C-terminal domain of yeast Nup133 (ScNup133), a component of the heptameric Nup84 subcomplex. Expression tests yielded ScNup133(944-1157) that produced crystals diffracting to 1.9A resolution. ScNup133(944-1157) adopts essentially an all alpha-helical fold, with a short two stranded beta-sheet at the C-terminus. The 11 alpha-helices of ScNup133(944-1157) form a compact fold. In contrast, the previously determined structure of human Nup133(934-1156) bound to a fragment of human Nup107 has its constituent alpha-helices are arranged in two globular blocks. These differences may reflect structural divergence among homologous nucleoporins.
+Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.,Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. PMID:21365675<ref>PMID:21365675</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3kfo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nucleoporin 3D structures|Nucleoporin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Almo, S]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Atwell, S]]
+[[Category: Almo SC]]
-[[Category: Bain, K]]
+[[Category: Atwell S]]
-[[Category: Bonanno, J B]]
+[[Category: Bain K]]
-[[Category: Burley, S K]]
+[[Category: Bonanno JB]]
-[[Category: Dickey, M]]
+[[Category: Burley SK]]
-[[Category: Emtage, J S]]
+[[Category: Dickey M]]
-[[Category: Fernandez-Martinez, J]]
+[[Category: Emtage JS]]
-[[Category: Franke, J D]]
+[[Category: Fernandez-Martinez J]]
-[[Category: Gheyi, T]]
+[[Category: Franke JD]]
-[[Category: Miller, S]]
+[[Category: Gheyi T]]
-[[Category: Structural genomic]]
+[[Category: Miller S]]
-[[Category: Phillips, J]]
+[[Category: Phillips J]]
-[[Category: Pieper, U]]
+[[Category: Pieper U]]
-[[Category: Rout, M]]
+[[Category: Rout M]]
-[[Category: Sali, A]]
+[[Category: Sali A]]
-[[Category: Sampathkumar, P]]
+[[Category: Sampathkumar P]]
-[[Category: Sauder, J M]]
+[[Category: Sauder JM]]
-[[Category: Thompson, D A]]
+[[Category: Thompson DA]]
-[[Category: Wasserman, S]]
+[[Category: Wasserman S]]
-[[Category: Membrane]]
-[[Category: Mrna transport]]
-[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-[[Category: Nuclear pore complex]]
-[[Category: Nucleus]]
-[[Category: Nup133]]
-[[Category: Phosphoprotein]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Protein transport]]
-[[Category: Proteolysis]]
-[[Category: Translocation]]
-[[Category: Transport]]
-[[Category: Yeast]]

3kfo

From Proteopedia

Current revision

Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae

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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