1vec

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein

Structural highlights

1vec is a 2 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 2.01Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

DDX6_HUMAN Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).

Function

DDX6_HUMAN In the process of mRNA degradation, may play a role in mRNA decapping.

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

Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.

Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes.,Matsui T, Hogetsu K, Usukura J, Sato T, Kumasaka T, Akao Y, Tanaka N Genes Cells. 2006 Apr;11(4):439-52. PMID:16611246^[1]

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

References

↑ Matsui T, Hogetsu K, Usukura J, Sato T, Kumasaka T, Akao Y, Tanaka N. Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes. Genes Cells. 2006 Apr;11(4):439-52. PMID:16611246 doi:10.1111/j.1365-2443.2006.00951.x

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/1vec"

@@ Line 3: / Line 3: @@
 <StructureSection load='1vec' size='340' side='right'caption='[[1vec]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vec]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1VEC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vec]] is a 2 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=1VEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.01&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qde|1qde]], [[1qva|1qva]], [[1q0u|1q0u]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HUMRCK ([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'>[https://proteopedia.org/fgij/fg.htm?mol=1vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vec OCA], [https://pdbe.org/1vec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vec RCSB], [https://www.ebi.ac.uk/pdbsum/1vec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vec ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vec OCA], [http://pdbe.org/1vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vec RCSB], [http://www.ebi.ac.uk/pdbsum/1vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vec ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN]] Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).
+[https://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN] Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).
 == Function ==
-[[http://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN]] In the process of mRNA degradation, may play a role in mRNA decapping.
+[https://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN] In the process of mRNA degradation, may play a role in mRNA decapping.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 17: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ve/1vec_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 39: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Hogetsu, K]]
+[[Category: Hogetsu K]]
-[[Category: Kumasaka, T]]
+[[Category: Kumasaka T]]
-[[Category: Matsui, T]]
+[[Category: Matsui T]]
-[[Category: Sato, T]]
+[[Category: Sato T]]
-[[Category: Tanaka, M]]
+[[Category: Tanaka M]]
-[[Category: Tanaka, N]]
+[[Category: Tanaka N]]
-[[Category: Yukihiro, Y]]
+[[Category: Yukihiro Y]]
-[[Category: Dead-box protein]]
-[[Category: Rna binding protein]]
-[[Category: Rna helicase]]

1vec

From Proteopedia

Current revision

Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein

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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