3w5k

From Proteopedia

(Difference between revisions)

Revision as of 01:16, 25 December 2014

Crystal structure of Snail1 and importin beta complex

Structural highlights

3w5k is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	KPNB1, NTF97 (HUMAN), SNAI1, SNAH (HUMAN)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[IMB1_HUMAN] Functions in nuclear protein import, either in association with an adapter protein, like an importin-alpha subunit, which binds to nuclear localization signals (NLS) in cargo substrates, or by acting as autonomous nuclear transport receptor. Acting autonomously, serves itself as NLS receptor. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates autonomously the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In association with IPO7 mediates the nuclear import of H1 histone. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev. Imports PRKCI into the nucleus.^[1] ^[2] ^[3] [SNAI1_HUMAN] Involved in induction of the epithelial to mesenchymal transition (EMT), formation and maintenance of embryonic mesoderm, growth arrest, survival and cell migration. Binds to 3 E-boxes of the E-cadherin/CDH1 gene promoter and to the promoters of CLDN7 and KRT8 and, in association with histone demethylase KDM1A which it recruits to the promoters, causes a decrease in dimethylated H3K4 levels and represses transcription. Associates with EGR1 and SP1 to mediate tetradecanoyl phorbol acetate (TPA)-induced up-regulation of CDKN2B, possibly by binding to the CDKN2B promoter region 5'-TCACA-3. In addition, may also activate the CDKN2B promoter by itself.^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Snail contributes to the epithelial-mesenchymal transition by suppressing E-cadherin in transcription processes. The Snail C2H2-type zinc-finger (ZF) domain functions both as a nuclear localization signal which binds to importin beta directly and as a DNA-binding domain. Here, a 2.5 A resolution structure of four ZF domains of Snail1 complexed with importin beta is presented. The X-ray structure reveals that the four ZFs of Snail1 are required for tight binding to importin beta in the nuclear import of Snail1. The shape of the ZFs in the X-ray structure is reminiscent of a round snail, where ZF1 represents the head, ZF2-ZF4 the shell, showing a novel interaction mode, and the five C-terminal residues the tail. Although there are many kinds of C2H2-type ZFs which have the same fold as Snail, nuclear import by direct recognition of importin beta is observed in a limited number of C2H2-type ZF proteins such as Snail, Wt1, KLF1 and KLF8, which have the common feature of terminating in ZF domains with a short tail of amino acids.

Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin beta.,Choi S, Yamashita E, Yasuhara N, Song J, Son SY, Won YH, Hong HR, Shin YS, Sekimoto T, Park IY, Yoneda Y, Lee SJ Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1050-60. doi:, 10.1107/S1399004714000972. Epub 2014 Mar 19. PMID:24699649^[10]

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

References

↑ Jakel S, Gorlich D. Importin beta, transportin, RanBP5 and RanBP7 mediate nuclear import of ribosomal proteins in mammalian cells. EMBO J. 1998 Aug 3;17(15):4491-502. PMID:9687515 doi:10.1093/emboj/17.15.4491
↑ Jakel S, Albig W, Kutay U, Bischoff FR, Schwamborn K, Doenecke D, Gorlich D. The importin beta/importin 7 heterodimer is a functional nuclear import receptor for histone H1. EMBO J. 1999 May 4;18(9):2411-23. PMID:10228156 doi:10.1093/emboj/18.9.2411
↑ White WO, Seibenhener ML, Wooten MW. Phosphorylation of tyrosine 256 facilitates nuclear import of atypical protein kinase C. J Cell Biochem. 2002;85(1):42-53. PMID:11891849
↑ Batlle E, Sancho E, Franci C, Dominguez D, Monfar M, Baulida J, Garcia De Herreros A. The transcription factor snail is a repressor of E-cadherin gene expression in epithelial tumour cells. Nat Cell Biol. 2000 Feb;2(2):84-9. PMID:10655587 doi:http://dx.doi.org/10.1038/35000034
↑ Peinado H, Del Carmen Iglesias-de la Cruz M, Olmeda D, Csiszar K, Fong KS, Vega S, Nieto MA, Cano A, Portillo F. A molecular role for lysyl oxidase-like 2 enzyme in snail regulation and tumor progression. EMBO J. 2005 Oct 5;24(19):3446-58. Epub 2005 Aug 18. PMID:16096638 doi:http://dx.doi.org/10.1038/sj.emboj.7600781
↑ Yook JI, Li XY, Ota I, Fearon ER, Weiss SJ. Wnt-dependent regulation of the E-cadherin repressor snail. J Biol Chem. 2005 Mar 25;280(12):11740-8. Epub 2005 Jan 11. PMID:15647282 doi:http://dx.doi.org/10.1074/jbc.M413878200
↑ Hu CT, Chang TY, Cheng CC, Liu CS, Wu JR, Li MC, Wu WS. Snail associates with EGR-1 and SP-1 to upregulate transcriptional activation of p15INK4b. FEBS J. 2010 Mar;277(5):1202-18. doi: 10.1111/j.1742-4658.2009.07553.x. Epub 2010, Feb 1. PMID:20121949 doi:http://dx.doi.org/10.1111/j.1742-4658.2009.07553.x
↑ Lin T, Ponn A, Hu X, Law BK, Lu J. Requirement of the histone demethylase LSD1 in Snai1-mediated transcriptional repression during epithelial-mesenchymal transition. Oncogene. 2010 Sep 2;29(35):4896-904. doi: 10.1038/onc.2010.234. Epub 2010 Jun, 21. PMID:20562920 doi:http://dx.doi.org/10.1038/onc.2010.234
↑ Zhang K, Rodriguez-Aznar E, Yabuta N, Owen RJ, Mingot JM, Nojima H, Nieto MA, Longmore GD. Lats2 kinase potentiates Snail1 activity by promoting nuclear retention upon phosphorylation. EMBO J. 2012 Jan 4;31(1):29-43. doi: 10.1038/emboj.2011.357. Epub 2011 Sep 27. PMID:21952048 doi:http://dx.doi.org/10.1038/emboj.2011.357
↑ Choi S, Yamashita E, Yasuhara N, Song J, Son SY, Won YH, Hong HR, Shin YS, Sekimoto T, Park IY, Yoneda Y, Lee SJ. Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin beta. Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1050-60. doi:, 10.1107/S1399004714000972. Epub 2014 Mar 19. PMID:24699649 doi:http://dx.doi.org/10.1107/S1399004714000972

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3w5k"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3w5k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W5K FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KPNB1, NTF97 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SNAI1, SNAH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KPNB1, NTF97 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SNAI1, SNAH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3w5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w5k RCSB], [http://www.ebi.ac.uk/pdbsum/3w5k PDBsum]</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=3w5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w5k RCSB], [http://www.ebi.ac.uk/pdbsum/3w5k PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/IMB1_HUMAN IMB1_HUMAN]] Functions in nuclear protein import, either in association with an adapter protein, like an importin-alpha subunit, which binds to nuclear localization signals (NLS) in cargo substrates, or by acting as autonomous nuclear transport receptor. Acting autonomously, serves itself as NLS receptor. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates autonomously the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In association with IPO7 mediates the nuclear import of H1 histone. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev. Imports PRKCI into the nucleus.<ref>PMID:9687515</ref> <ref>PMID:10228156</ref> <ref>PMID:11891849</ref>  [[http://www.uniprot.org/uniprot/SNAI1_HUMAN SNAI1_HUMAN]] Involved in induction of the epithelial to mesenchymal transition (EMT), formation and maintenance of embryonic mesoderm, growth arrest, survival and cell migration. Binds to 3 E-boxes of the E-cadherin/CDH1 gene promoter and to the promoters of CLDN7 and KRT8 and, in association with histone demethylase KDM1A which it recruits to the promoters, causes a decrease in dimethylated H3K4 levels and represses transcription. Associates with EGR1 and SP1 to mediate tetradecanoyl phorbol acetate (TPA)-induced up-regulation of CDKN2B, possibly by binding to the CDKN2B promoter region 5'-TCACA-3. In addition, may also activate the CDKN2B promoter by itself.<ref>PMID:10655587</ref> <ref>PMID:16096638</ref> <ref>PMID:15647282</ref> <ref>PMID:20121949</ref> <ref>PMID:20562920</ref> <ref>PMID:21952048</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 13: / Line 15: @@
 Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin beta.,Choi S, Yamashita E, Yasuhara N, Song J, Son SY, Won YH, Hong HR, Shin YS, Sekimoto T, Park IY, Yoneda Y, Lee SJ Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1050-60. doi:, 10.1107/S1399004714000972. Epub 2014 Mar 19. PMID:24699649<ref>PMID:24699649</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+==See Also==
+*[[Importin|Importin]]
 == References ==
 <references/>
@@ Line 20: / Line 25: @@
 </StructureSection>
 [[Category: Human]]
-[[Category: Choi, S.]]
+[[Category: Choi, S]]
-[[Category: Lee, S J.]]
+[[Category: Lee, S J]]
-[[Category: Park, I Y.]]
+[[Category: Park, I Y]]
-[[Category: Sekimoto, T.]]
+[[Category: Sekimoto, T]]
-[[Category: Shin, Y S.]]
+[[Category: Shin, Y S]]
-[[Category: Son, S Y.]]
+[[Category: Son, S Y]]
-[[Category: Song, J.]]
+[[Category: Song, J]]
-[[Category: Won, Y H.]]
+[[Category: Won, Y H]]
-[[Category: Yamashita, E.]]
+[[Category: Yamashita, E]]
-[[Category: Yasuhara, N.]]
+[[Category: Yasuhara, N]]
-[[Category: Yoneda, Y.]]
+[[Category: Yoneda, Y]]
 [[Category: Importin beta]]
 [[Category: Nuclear protein-metal binding protein complex]]
 [[Category: Nuclear transport factor snail1]]
 [[Category: Transcription repressor]]

3w5k

From Proteopedia

Revision as of 01:16, 25 December 2014

Crystal structure of Snail1 and importin beta complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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