1m19: Difference between revisions

Latest revision as of 07:57, 15 November 2023

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Structural highlights

1m19 is a 10 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 2.3Å
Ligands:	ABU, BAL, DIB, IMT, MN, PYB
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H3C_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

We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.

Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands.,Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K J Mol Biol. 2003 Feb 14;326(2):371-80. PMID:12559907^[1]

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

References

↑ Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol. 2003 Feb 14;326(2):371-80. PMID:12559907

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OCA

[1] Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol. 2003 Feb 14;326(2):371-80. PMID:12559907

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='1m19' size='340' side='right'caption='[[1m19]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m19]] is a 10 chain structure with sequence from [https://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=1M19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M19 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1m19]] is a 10 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=1M19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M19 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=BAL:BETA-ALANINE'>BAL</scene>, <scene name='pdbligand=DIB:3-AMINO-(DIMETHYLPROPYLAMINE)'>DIB</scene>, <scene name='pdbligand=IMT:4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC+ACID'>IMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PYB:4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC+ACID'>PYB</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]] 2.3&#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;'>[[1aoi|1aoi]], [[1m18|1m18]], [[1m1a|1m1a]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=BAL:BETA-ALANINE'>BAL</scene>, <scene name='pdbligand=DIB:3-AMINO-(DIMETHYLPROPYLAMINE)'>DIB</scene>, <scene name='pdbligand=IMT:4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC+ACID'>IMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PYB:4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC+ACID'>PYB</scene></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=1m19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m19 OCA], [https://pdbe.org/1m19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m19 RCSB], [https://www.ebi.ac.uk/pdbsum/1m19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m19 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/H2A1_XENLA H2A1_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. [[https://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.
+[https://www.uniprot.org/uniprot/H3C_XENLA H3C_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 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: African clawed frog]]
 [[Category: Large Structures]]
-[[Category: Dervan, P B]]
+[[Category: Xenopus laevis]]
-[[Category: Edayathumangalam, R S]]
+[[Category: Dervan PB]]
-[[Category: Gottesfeld, J M]]
+[[Category: Edayathumangalam RS]]
-[[Category: Luger, K]]
+[[Category: Gottesfeld JM]]
-[[Category: Melander, C]]
+[[Category: Luger K]]
-[[Category: Suto, R K]]
+[[Category: Melander C]]
-[[Category: White, C L]]
+[[Category: Suto RK]]
-[[Category: Chromatin]]
+[[Category: White CL]]
-[[Category: Chromatin remodeling]]
-[[Category: Dna regognition]]
-[[Category: Histone]]
-[[Category: Nucleosome]]
-[[Category: Pyrrole-imidazole polyamide]]
-[[Category: Structural protein-dna complex]]

1m19: Difference between revisions

Latest revision as of 07:57, 15 November 2023

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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