2rb4

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the Helicase domain of human DDX25 RNA helicase

Structural highlights

2rb4 is a 2 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 2g2j. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDX25_HUMAN ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).^[1]

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^[2]

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

References

↑ Tang PZ, Tsai-Morris CH, Dufau ML. A novel gonadotropin-regulated testicular RNA helicase. A new member of the dead-box family. J Biol Chem. 1999 Dec 31;274(53):37932-40. PMID:10608860
↑ 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/2rb4"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Helicase domain of human DDX25 RNA helicase==
-<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='2rb4' size='340' side='right'caption='[[2rb4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([http://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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://pdbe.org/2rb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 ProSAT]</span></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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [https://pdbe.org/2rb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN]] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>
+[https://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</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/rb/2rb4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rb4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 2rb4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[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: Edwards, A M]]
+[[Category: Edwards AM]]
-[[Category: Ehn, M]]
+[[Category: Ehn M]]
-[[Category: Flodin, S]]
+[[Category: Flodin S]]
-[[Category: Flores, A]]
+[[Category: Flores A]]
-[[Category: Graslund, S]]
+[[Category: Graslund S]]
-[[Category: Hallberg, B M]]
+[[Category: Hallberg BM]]
-[[Category: Hammarstrom, M]]
+[[Category: Hammarstrom M]]
-[[Category: Hogbom, M]]
+[[Category: Hogbom M]]
-[[Category: Holmberg-Schiavone, L]]
+[[Category: Holmberg-Schiavone L]]
-[[Category: Kotenyova, T]]
+[[Category: Kotenyova T]]
-[[Category: Lehtio, L]]
+[[Category: Lehtio L]]
-[[Category: Nilsson-Ehle, P]]
+[[Category: Nilsson-Ehle P]]
-[[Category: Nordlund, P]]
+[[Category: Nordlund P]]
-[[Category: Nyman, T]]
+[[Category: Nyman T]]
-[[Category: Ogg, D]]
+[[Category: Ogg D]]
-[[Category: Persson, C]]
+[[Category: Persson C]]
-[[Category: Structural genomic]]
+[[Category: Sagemark J]]
-[[Category: Sagemark, J]]
+[[Category: Stenmark P]]
-[[Category: Stenmark, P]]
+[[Category: Sundstrom M]]
-[[Category: Sundstrom, M]]
+[[Category: Thorsell AG]]
-[[Category: Thorsell, A G]]
+[[Category: Uppenberg J]]
-[[Category: Uppenberg, J]]
+[[Category: Van den Berg S]]
-[[Category: Weigelt, J]]
+[[Category: Weigelt J]]
-[[Category: Alternative initiation]]
-[[Category: Atp-binding]]
-[[Category: Developmental protein]]
-[[Category: Differentiation]]
-[[Category: Hydrolase]]
-[[Category: Mrna transport]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphorylation]]
-[[Category: Rna helicase]]
-[[Category: Rna-binding]]
-[[Category: Rossmann fold]]
-[[Category: Sgc]]
-[[Category: Spermatogenesis]]
-[[Category: Translation regulation]]
-[[Category: Transport]]

2rb4

From Proteopedia

Current revision

Crystal structure of the Helicase domain of human DDX25 RNA helicase

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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