3u21

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution

Structural highlights

3u21 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.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NFRKB_HUMAN Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'.^[1] Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Modulates the deubiquitinase activity of UCHL5 in the INO80 complex.^[2]

Publication Abstract from PubMed

The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full length NFRKB is predicted to be around 65% disordered, comparative sequence analysis identified several potentially structured sections in the N-terminal region of the protein. These regions were targeted for crystallographic studies, and the structure of one of these regions spanning residues 370-495 was determined using the JCSG high-throughput structure determination pipeline. The structure reveals a novel, mostly helical domain reminiscent of the winged-helix fold typically involved in DNA binding. However, further analysis shows that this domain does not bind DNA, suggesting it may belong to a small group of winged-helix domains involved in protein-protein interactions.

Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein.,Kumar A, Mocklinghoff S, Yumoto F, Jaroszewski L, Farr CL, Grzechnik A, Nguyen P, Weichenberger CX, Chiu HJ, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Conklin BR, Fletterick RJ, Wilson IA PLoS One. 2012;7(9):e43761. Epub 2012 Sep 11. PMID:22984442^[3]

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

References

↑ Yao T, Song L, Jin J, Cai Y, Takahashi H, Swanson SK, Washburn MP, Florens L, Conaway RC, Cohen RE, Conaway JW. Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Mol Cell. 2008 Sep 26;31(6):909-17. doi: 10.1016/j.molcel.2008.08.027. PMID:18922472 doi:10.1016/j.molcel.2008.08.027
↑ Yao T, Song L, Jin J, Cai Y, Takahashi H, Swanson SK, Washburn MP, Florens L, Conaway RC, Cohen RE, Conaway JW. Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Mol Cell. 2008 Sep 26;31(6):909-17. doi: 10.1016/j.molcel.2008.08.027. PMID:18922472 doi:10.1016/j.molcel.2008.08.027
↑ Kumar A, Mocklinghoff S, Yumoto F, Jaroszewski L, Farr CL, Grzechnik A, Nguyen P, Weichenberger CX, Chiu HJ, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Conklin BR, Fletterick RJ, Wilson IA. Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein. PLoS One. 2012;7(9):e43761. Epub 2012 Sep 11. PMID:22984442 doi:http://dx.doi.org/10.1371/journal.pone.0043761

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3u21"

Categories: Homo sapiens | Large Structures | Partnership for Stem Cell Biology

@@ Line 3: / Line 3: @@
 <StructureSection load='3u21' size='340' side='right'caption='[[3u21]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3u21]] is a 2 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=3U21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U21 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3u21]] 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=3U21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U21 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC063280, INO80G, NFRKB ([https://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=3u21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u21 OCA], [https://pdbe.org/3u21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u21 RCSB], [https://www.ebi.ac.uk/pdbsum/3u21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u21 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NFRKB_HUMAN NFRKB_HUMAN]] Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'.<ref>PMID:18922472</ref>   Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Modulates the deubiquitinase activity of UCHL5 in the INO80 complex.<ref>PMID:18922472</ref>
+[https://www.uniprot.org/uniprot/NFRKB_HUMAN NFRKB_HUMAN] Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'.<ref>PMID:18922472</ref>   Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Modulates the deubiquitinase activity of UCHL5 in the INO80 complex.<ref>PMID:18922472</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Biology, Partnership for Stem Cell]]
+[[Category: Partnership for Stem Cell Biology]]
-[[Category: Structural genomic]]
-[[Category: STEMCELL, Partnership for Stem Cell Biology]]
-[[Category: Dna binding]]
-[[Category: Dna binding protein]]
-[[Category: Dna/rna-binding 3-helical bundle]]
-[[Category: Jcsg]]
-[[Category: Partnership for stem cell biology]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Psi-biology]]
-[[Category: Stemcell]]
-[[Category: Transcription regulation]]
-[[Category: Winged-hth domain]]

3u21

From Proteopedia

Current revision

Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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