3lel

From Proteopedia

(Difference between revisions)

Current revision

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

Structural highlights

3lel is a 20 chain structure with sequence from Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.95Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H32_XENLA Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

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

Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

Structural insight into the sequence dependence of nucleosome positioning.,Wu B, Mohideen K, Vasudevan D, Davey CA Structure. 2010 Mar 14;18(4):528-36. PMID:20399189^[1]

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

References

↑ Wu B, Mohideen K, Vasudevan D, Davey CA. Structural insight into the sequence dependence of nucleosome positioning. Structure. 2010 Mar 14;18(4):528-36. PMID:20399189 doi:10.1016/j.str.2010.01.015

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/3lel"

Categories: Large Structures | Xenopus laevis | Davey CA | Vasudevan D | Wu B

@@ Line 1: / Line 1: @@
 ==Structural Insight into the Sequence-Dependence of Nucleosome Positioning==
-<StructureSection load='3lel' size='340' side='right' caption='[[3lel]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+<StructureSection load='3lel' size='340' side='right'caption='[[3lel]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lel]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LEL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lel]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LEL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kx5|1kx5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3lel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lel OCA], [http://pdbe.org/3lel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lel RCSB], [http://www.ebi.ac.uk/pdbsum/3lel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lel ProSAT]</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=3lel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lel OCA], [https://pdbe.org/3lel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lel RCSB], [https://www.ebi.ac.uk/pdbsum/3lel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lel ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/H2B11_XENLA H2B11_XENLA]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [[http://www.uniprot.org/uniprot/H32_XENLA H32_XENLA]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [[http://www.uniprot.org/uniprot/H4_XENLA H4_XENLA]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
+[https://www.uniprot.org/uniprot/H32_XENLA H32_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Histone|Histone]]
+*[[Histone 3D structures|Histone 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: African clawed frog]]
+[[Category: Large Structures]]
-[[Category: Davey, C A]]
+[[Category: Xenopus laevis]]
-[[Category: Vasudevan, D]]
+[[Category: Davey CA]]
-[[Category: Wu, B]]
+[[Category: Vasudevan D]]
-[[Category: Acetylation]]
+[[Category: Wu B]]
-[[Category: Chromatin]]
-[[Category: Chromosomal protein]]
-[[Category: Dna flexibility]]
-[[Category: Dna-binding]]
-[[Category: Methylation]]
-[[Category: Nucleosome]]
-[[Category: Nucleosome core]]
-[[Category: Nucleosome positioning]]
-[[Category: Nucleus]]
-[[Category: Structural protein-dna complex]]

3lel

From Proteopedia

Current revision

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

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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