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2kdo

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Revision as of 10:12, 18 July 2018

Warning: this is a large structure, and loading might take a long time or not happen at all.

Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS

Structural highlights

2kdo is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	SBDS, CGI-97 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Warning: this is a large structure, and loading might take a long time or not happen at all.

Disease

[SBDS_HUMAN] Idiopathic aplastic anemia;Shwachman-Diamond syndrome. The disease is caused by mutations affecting the gene represented in this entry.^[1] ^[2]

Function

[SBDS_HUMAN] Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFTUD1, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell proliferation.^[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

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS.

Structure, dynamics, and RNA interaction analysis of the human SBDS protein.,de Oliveira JF, Sforca ML, Blumenschein TM, Goldfeder MB, Guimaraes BG, Oliveira CC, Zanchin NI, Zeri AC J Mol Biol. 2010 Mar 5;396(4):1053-69. Epub 2010 Jan 4. PMID:20053358^[7]

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

References

↑ Finch AJ, Hilcenko C, Basse N, Drynan LF, Goyenechea B, Menne TF, Gonzalez Fernandez A, Simpson P, D'Santos CS, Arends MJ, Donadieu J, Bellanne-Chantelot C, Costanzo M, Boone C, McKenzie AN, Freund SM, Warren AJ. Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev. 2011 May 1;25(9):917-29. PMID:21536732 doi:10.1101/gad.623011
↑ Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Nat Genet. 2003 Jan;33(1):97-101. Epub 2002 Dec 23. PMID:12496757 doi:http://dx.doi.org/10.1038/ng1062
↑ Hesling C, Oliveira CC, Castilho BA, Zanchin NI. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. Exp Cell Res. 2007 Dec 10;313(20):4180-95. Epub 2007 Jul 10. PMID:17643419 doi:10.1016/j.yexcr.2007.06.024
↑ Ball HL, Zhang B, Riches JJ, Gandhi R, Li J, Rommens JM, Myers JS. Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses. Hum Mol Genet. 2009 Oct 1;18(19):3684-95. doi: 10.1093/hmg/ddp316. Epub 2009 Jul , 14. PMID:19602484 doi:http://dx.doi.org/10.1093/hmg/ddp316
↑ Orelio C, Verkuijlen P, Geissler J, van den Berg TK, Kuijpers TW. SBDS expression and localization at the mitotic spindle in human myeloid progenitors. PLoS One. 2009 Sep 17;4(9):e7084. doi: 10.1371/journal.pone.0007084. PMID:19759903 doi:http://dx.doi.org/10.1371/journal.pone.0007084
↑ Finch AJ, Hilcenko C, Basse N, Drynan LF, Goyenechea B, Menne TF, Gonzalez Fernandez A, Simpson P, D'Santos CS, Arends MJ, Donadieu J, Bellanne-Chantelot C, Costanzo M, Boone C, McKenzie AN, Freund SM, Warren AJ. Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev. 2011 May 1;25(9):917-29. PMID:21536732 doi:10.1101/gad.623011
↑ de Oliveira JF, Sforca ML, Blumenschein TM, Goldfeder MB, Guimaraes BG, Oliveira CC, Zanchin NI, Zeri AC. Structure, dynamics, and RNA interaction analysis of the human SBDS protein. J Mol Biol. 2010 Mar 5;396(4):1053-69. Epub 2010 Jan 4. PMID:20053358 doi:10.1016/j.jmb.2009.12.039

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2kdo"

@@ Line 1: / Line 1: @@
+{{Large structure}}
 ==Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS==
 <StructureSection load='2kdo' size='340' side='right' caption='[[2kdo]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[2kdo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDO FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SBDS, CGI-97 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2kdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdo OCA], [http://pdbe.org/2kdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kdo RCSB], [http://www.ebi.ac.uk/pdbsum/2kdo 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=2kdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdo OCA], [http://pdbe.org/2kdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kdo RCSB], [http://www.ebi.ac.uk/pdbsum/2kdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdo ProSAT]</span></td></tr>
 </table>
 {{Large structure}}
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kdo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kdo_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2kdo

From Proteopedia

Revision as of 10:12, 18 July 2018

Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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