3ber: Difference between revisions

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{{Seed}}
[[Image:3ber.png|left|200px]]


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==Human DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP==
The line below this paragraph, containing "STRUCTURE_3ber", creates the "Structure Box" on the page.
<StructureSection load='3ber' size='340' side='right'caption='[[3ber]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3ber]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BER FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_3ber|  PDB=3ber  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ber FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ber OCA], [https://pdbe.org/3ber PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ber RCSB], [https://www.ebi.ac.uk/pdbsum/3ber PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ber ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DDX47_HUMAN DDX47_HUMAN] Involved in apoptosis. May have a role in rRNA processing and mRNA splicing. Associates with pre-rRNA precursors.<ref>PMID:15977068</ref> <ref>PMID:16963496</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/be/3ber_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/main_output.php?pdb_ID=3ber ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.


===Human DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP===
Comparative structural analysis of human DEAD-box RNA helicases.,Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364<ref>PMID:20941364</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ber" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_20941364}}, adds the Publication Abstract to the page
*[[Helicase 3D structures|Helicase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 20941364 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20941364}}
__TOC__
 
</StructureSection>
==About this Structure==
3BER is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BER OCA].
 
==Reference==
<ref group="xtra">PMID:20941364</ref><references group="xtra"/>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Arrowsmith, C H.]]
[[Category: Large Structures]]
[[Category: Berg, S Van Den.]]
[[Category: Arrowsmith CH]]
[[Category: Berglund, H.]]
[[Category: Berglund H]]
[[Category: Busam, R D.]]
[[Category: Busam RD]]
[[Category: Collins, R.]]
[[Category: Collins R]]
[[Category: Dahlgren, L G.]]
[[Category: Dahlgren LG]]
[[Category: Edwards, A M.]]
[[Category: Edwards AM]]
[[Category: Flodin, S.]]
[[Category: Flodin S]]
[[Category: Flores, A.]]
[[Category: Flores A]]
[[Category: Graslund, S.]]
[[Category: Graslund S]]
[[Category: Hammarstrom, M.]]
[[Category: Hammarstrom M]]
[[Category: Holmberg-Schiavone, L.]]
[[Category: Holmberg-Schiavone L]]
[[Category: Johansson, I.]]
[[Category: Johansson I]]
[[Category: Kallas, A.]]
[[Category: Kallas A]]
[[Category: Karlberg, T.]]
[[Category: Karlberg T]]
[[Category: Kotenyova, T.]]
[[Category: Kotenyova T]]
[[Category: Lehtio, L.]]
[[Category: Lehtio L]]
[[Category: Moche, M.]]
[[Category: Moche M]]
[[Category: Nilsson, M E.]]
[[Category: Nilsson ME]]
[[Category: Nordlund, P.]]
[[Category: Nordlund P]]
[[Category: Nyman, T.]]
[[Category: Nyman T]]
[[Category: Persson, C.]]
[[Category: Persson C]]
[[Category: SGC, Structural Genomics Consortium.]]
[[Category: Sagemark J]]
[[Category: Sagemark, J.]]
[[Category: Svensson L]]
[[Category: Svensson, L.]]
[[Category: Thorsell AG]]
[[Category: Thorsell, A G.]]
[[Category: Tresaugues L]]
[[Category: Tresaugues, L.]]
[[Category: Van Den Berg S]]
[[Category: Weigelt, J.]]
[[Category: Weigelt J]]
[[Category: Welin, M.]]
[[Category: Welin M]]
[[Category: Amp]]
[[Category: Atp-binding]]
[[Category: Dead]]
[[Category: Hydrolase]]
[[Category: Nucleotide-binding]]
[[Category: Nucleus]]
[[Category: Rna helicase]]
[[Category: Rna-binding]]
[[Category: Sgc]]
[[Category: Structural genomic]]
[[Category: Structural genomics consortium]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 11:37:36 2010''

Latest revision as of 15:08, 30 August 2023

Human DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMPHuman DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP

Structural highlights

3ber is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDX47_HUMAN Involved in apoptosis. May have a role in rRNA processing and mRNA splicing. Associates with pre-rRNA precursors.[1] [2]

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

DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

Comparative structural analysis of human DEAD-box RNA helicases.,Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364[3]

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

See Also

References

  1. ↑ Lee JH, Rho SB, Chun T. GABAA receptor-associated protein (GABARAP) induces apoptosis by interacting with DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 47 (DDX 47). Biotechnol Lett. 2005 May;27(9):623-8. PMID:15977068 doi:http://dx.doi.org/10.1007/s10529-005-3628-2
  2. ↑ Sekiguchi T, Hayano T, Yanagida M, Takahashi N, Nishimoto T. NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47. Nucleic Acids Res. 2006;34(16):4593-608. Epub 2006 Sep 8. PMID:16963496 doi:http://dx.doi.org/10.1093/nar/gkl603
  3. ↑ Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H. Comparative structural analysis of human DEAD-box RNA helicases. PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364 doi:10.1371/journal.pone.0012791

3ber, resolution 1.40Å

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