2jx2: Difference between revisions

Latest revision as of 09:42, 9 May 2024

Solution conformation of RNA-bound NELF-E RRM

Structural highlights

2jx2 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NELFE_HUMAN Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex.^[1] ^[2] ^[3]

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

The E subunit of the human heterotetrameric negative transcription elongation factor (NELF-E) contains a canonical betaalphabetabetaalphabeta RNA recognition motif (RRM) that binds to a wide variety of RNA sequences. These induce very similar conformational changes in the RRM as determined by nuclear magnetic resonance spectroscopy. Although the RNA binding interface of a canonical RRM is mainly located at its beta-sheet surface, for NELF-E RRM large chemical shift perturbations are observed for residues in the flexible C-terminal region and the loop between beta 3 and alpha 2, and both regions are distant from the interface. We determined the solution structure of single-stranded transactivator responsive element (TAR) RNA-bound NELF-E RRM. This structure clearly shows that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus. The RNA-bound form of NELF-E RRM is very similar to the RNA-bound form of U1A RRM, although the C-terminus of the NELF-E RRM is unstructured in the free protein, whereas it is helical in the U1A protein. Thus, RNA binding to NELF-E RRM induces a conformational change toward the U1A structure, resulting in highly similar RNA binding conformations for both proteins.

NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding.,Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P Biochemistry. 2008 Mar 25;47(12):3756-61. Epub 2008 Feb 28. PMID:18303858^[4]

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

References

↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
↑ Yamaguchi Y, Inukai N, Narita T, Wada T, Handa H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol. 2002 May;22(9):2918-27. PMID:11940650
↑ Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062
↑ Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P. NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding. Biochemistry. 2008 Mar 25;47(12):3756-61. Epub 2008 Feb 28. PMID:18303858 doi:10.1021/bi702429m

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401

[2] Yamaguchi Y, Inukai N, Narita T, Wada T, Handa H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol. 2002 May;22(9):2918-27. PMID:11940650

[3] Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062

[4] Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P. NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding. Biochemistry. 2008 Mar 25;47(12):3756-61. Epub 2008 Feb 28. PMID:18303858 doi:10.1021/bi702429m

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-[[Image:2jx2.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2jx2", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2jx2|  PDB=2jx2  |  SCENE=  }}
-'''Solution conformation of RNA-bound NELF-E RRM'''
+==Solution conformation of RNA-bound NELF-E RRM==
+<StructureSection load='2jx2' size='340' side='right'caption='[[2jx2]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2jx2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JX2 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2jx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jx2 OCA], [https://pdbe.org/2jx2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jx2 RCSB], [https://www.ebi.ac.uk/pdbsum/2jx2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jx2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NELFE_HUMAN NELFE_HUMAN] Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex.<ref>PMID:10199401</ref> <ref>PMID:11940650</ref> <ref>PMID:12612062</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/jx/2jx2_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=2jx2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The E subunit of the human heterotetrameric negative transcription elongation factor (NELF-E) contains a canonical betaalphabetabetaalphabeta RNA recognition motif (RRM) that binds to a wide variety of RNA sequences. These induce very similar conformational changes in the RRM as determined by nuclear magnetic resonance spectroscopy. Although the RNA binding interface of a canonical RRM is mainly located at its beta-sheet surface, for NELF-E RRM large chemical shift perturbations are observed for residues in the flexible C-terminal region and the loop between beta 3 and alpha 2, and both regions are distant from the interface. We determined the solution structure of single-stranded transactivator responsive element (TAR) RNA-bound NELF-E RRM. This structure clearly shows that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus. The RNA-bound form of NELF-E RRM is very similar to the RNA-bound form of U1A RRM, although the C-terminus of the NELF-E RRM is unstructured in the free protein, whereas it is helical in the U1A protein. Thus, RNA binding to NELF-E RRM induces a conformational change toward the U1A structure, resulting in highly similar RNA binding conformations for both proteins.
-==Overview==
+NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding.,Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P Biochemistry. 2008 Mar 25;47(12):3756-61. Epub 2008 Feb 28. PMID:18303858<ref>PMID:18303858</ref>
-The E subunit of the human heterotetrameric negative transcription elongation factor (NELF-E) contains a canonical betaalphabetabetaalphabeta RNA recognition motif (RRM) that binds to a wide variety of RNA sequences. These induce very similar conformational changes in the RRM as determined by nuclear magnetic resonance spectroscopy. Although the RNA binding interface of a canonical RRM is mainly located at its beta-sheet surface, for NELF-E RRM large chemical shift perturbations are observed for residues in the flexible C-terminal region and the loop between beta 3 and alpha 2, and both regions are distant from the interface. We determined the solution structure of single-stranded transactivator responsive element (TAR) RNA-bound NELF-E RRM. This structure clearly shows that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus. The RNA-bound form of NELF-E RRM is very similar to the RNA-bound form of U1A RRM, although the C-terminus of the NELF-E RRM is unstructured in the free protein, whereas it is helical in the U1A protein. Thus, RNA binding to NELF-E RRM induces a conformational change toward the U1A structure, resulting in highly similar RNA binding conformations for both proteins.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-JX2 is a [[Single protein]] structure of 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=2JX2 OCA].
+</div>
+<div class="pdbe-citations 2jx2" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding., Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P, Biochemistry. 2008 Mar 25;47(12):3756-61. Epub 2008 Feb 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18303858 18303858]
+*[[Negative elongation factor|Negative elongation factor]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Jampani, N.]]
+[[Category: Jampani N]]
-[[Category: Roesch, P.]]
+[[Category: Roesch P]]
-[[Category: Schweimer, K.]]
+[[Category: Schweimer K]]
-[[Category: Wenzel, S.]]
+[[Category: Wenzel S]]
-[[Category: Woehrl, B M.]]
+[[Category: Woehrl BM]]
-[[Category: Coiled coil]]
-[[Category: Nelfe-rrm]]
-[[Category: Nucleus]]
-[[Category: Phosphorylation]]
-[[Category: Repressor]]
-[[Category: Rna-binding]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Ubl conjugation]]

2jx2: Difference between revisions

Latest revision as of 09:42, 9 May 2024

Solution conformation of RNA-bound NELF-E RRM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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