1rly

From Proteopedia

(Difference between revisions)

Current revision

RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures)

Structural highlights

1rly 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, 25 models
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TF2B_HUMAN General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

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 general transcription factor, TFIIB, plays an important role in the assembly of the pre-initiation complex. The N-terminal domain (NTD) of TFIIB contains a zinc-ribbon motif, which is responsible for the recruitment of RNA polymerase II and TFIIF to the core promoter region. Although zinc-ribbon motif structures of eukaryotic and archaeal TFIIBs have been reported previously, the structural role of Zn2 binding to TFIIB remains to be determined. In the present paper, we report NMR and biochemical studies of human TFIIB NTD, which characterize the structure and dynamics of the TFIIB Zn2-binding domain in both Zn2-bound and -free states. The NMR data show that, whereas the backbone fold of NTD is pre-formed in the apo state, Zn2 binding reduces backbone mobility in the b-turn (Arg28-Gly30), induces enhanced structural rigidity of the charged-cluster domain in the central linker region of TFIIB and appends a positive surface charge within the Zn2-binding site. V8 protease-sensitivity assays of full-length TFIIB support the Zn2-dependent structural changes. These structural effects of Zn2 binding on TFIIB may have a critical role in interactions with its binding partners, such as the Rpb1 subunit of RNA polymerase II.

Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB.,Ghosh M, Elsby LM, Mal TK, Gooding JM, Roberts SG, Ikura M Biochem J. 2004 Mar 1;378(Pt 2):317-24. PMID:14641108^[1]

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

References

↑ Ghosh M, Elsby LM, Mal TK, Gooding JM, Roberts SG, Ikura M. Probing Zn2+-binding effects on the zinc-ribbon domain of human general transcription factor TFIIB. Biochem J. 2004 Mar 1;378(Pt 2):317-24. PMID:14641108 doi:10.1042/BJ20031706

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/1rly"

Categories: Homo sapiens | Large Structures | Ghosh M | Ikura M

@@ Line 1: / Line 1: @@
 ==RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures)==
-<StructureSection load='1rly' size='340' side='right' caption='[[1rly]], [[NMR_Ensembles_of_Models | 25 NMR models]]' scene=''>
+<StructureSection load='1rly' size='340' side='right'caption='[[1rly]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rly]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RLY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rly]] 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=1RLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RLY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">Solution NMR, 25 models</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GTF2B, TFIIB, TF2B ([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=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=1rly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rly OCA], [http://pdbe.org/1rly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rly RCSB], [http://www.ebi.ac.uk/pdbsum/1rly PDBsum]</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=1rly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rly OCA], [https://pdbe.org/1rly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rly RCSB], [https://www.ebi.ac.uk/pdbsum/1rly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rly ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TF2B_HUMAN TF2B_HUMAN]] General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
+[https://www.uniprot.org/uniprot/TF2B_HUMAN TF2B_HUMAN] General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
 == 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/rl/1rly_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rl/1rly_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 30: / Line 31: @@
 ==See Also==
-*[[Transcription initiation factor|Transcription initiation factor]]
+*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Ghosh, M]]
+[[Category: Large Structures]]
-[[Category: Ikura, M]]
+[[Category: Ghosh M]]
-[[Category: Metal binding protein]]
+[[Category: Ikura M]]
-[[Category: Rubredoxin knuckle]]
-[[Category: Zinc ribbon]]

1rly

From Proteopedia

Current revision

RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures)

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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