3dkp: Difference between revisions

Latest revision as of 12:48, 30 August 2023

Human DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP

Structural highlights

3dkp 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 2.1Å
Ligands:	ADP, GOL, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDX52_HUMAN

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^[1]

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

References

↑ 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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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]

@@ Line 3: / Line 3: @@
 <StructureSection load='3dkp' size='340' side='right'caption='[[3dkp]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dkp]] 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=3DKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dkp]] 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=3DKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.1&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DDX52, ROK1 ([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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkp OCA], [https://pdbe.org/3dkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkp RCSB], [https://www.ebi.ac.uk/pdbsum/3dkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DDX52_HUMAN DDX52_HUMAN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Andersson, J]]
+[[Category: Andersson J]]
-[[Category: Arrowsmith, C H]]
+[[Category: Arrowsmith CH]]
-[[Category: Berg, S van den]]
+[[Category: Berglund H]]
-[[Category: Berglund, H]]
+[[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: Johansson A]]
-[[Category: Johansson, A]]
+[[Category: Johansson I]]
-[[Category: Johansson, I]]
+[[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: Olesen K]]
-[[Category: Olesen, K]]
+[[Category: Persson C]]
-[[Category: Persson, C]]
+[[Category: Sagemark J]]
-[[Category: Structural genomic]]
+[[Category: Schueler H]]
-[[Category: Sagemark, J]]
+[[Category: Thorsell AG]]
-[[Category: Schueler, H]]
+[[Category: Tresaugues L]]
-[[Category: Thorsell, A G]]
+[[Category: Welin M]]
-[[Category: Tresaugues, L]]
+[[Category: Wikstrom M]]
-[[Category: Welin, M]]
+[[Category: Wisniewska M]]
-[[Category: Wikstrom, M]]
+[[Category: Van den Berg S]]
-[[Category: Wisniewska, M]]
-[[Category: Adp]]
-[[Category: Atp-binding]]
-[[Category: Dead]]
-[[Category: Hydrolase]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Rna helicase]]
-[[Category: Rna-binding]]
-[[Category: Rrna]]
-[[Category: Sgc]]

3dkp: Difference between revisions

Latest revision as of 12:48, 30 August 2023

Human DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools