3ber

From Proteopedia

(Difference between revisions)

Current revision

Human 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.

References

↑ 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
↑ 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
↑ 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

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/3ber"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ber' size='340' side='right'caption='[[3ber]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ber]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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>
+<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>
-</td></tr><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>
+</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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DDX47 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<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>
 <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>
+[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]]
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3ber" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Arrowsmith, C H]]
+[[Category: Arrowsmith CH]]
-[[Category: Berg, S Van Den]]
+[[Category: Berglund H]]
-[[Category: Berglund, H]]
+[[Category: Busam RD]]
-[[Category: Busam, R D]]
+[[Category: Collins R]]
-[[Category: Collins, R]]
+[[Category: Dahlgren LG]]
-[[Category: Dahlgren, L G]]
+[[Category: Edwards AM]]
-[[Category: Edwards, A M]]
+[[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 ME]]
-[[Category: Nilsson, M E]]
+[[Category: Nordlund P]]
-[[Category: Nordlund, P]]
+[[Category: Nyman T]]
-[[Category: Nyman, T]]
+[[Category: Persson C]]
-[[Category: Persson, C]]
+[[Category: Sagemark J]]
-[[Category: Structural genomic]]
+[[Category: Svensson L]]
-[[Category: Sagemark, J]]
+[[Category: Thorsell AG]]
-[[Category: Svensson, L]]
+[[Category: Tresaugues L]]
-[[Category: Thorsell, A G]]
+[[Category: Van Den Berg S]]
-[[Category: Tresaugues, L]]
+[[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]]

3ber

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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