5chl: Difference between revisions

Revision as of 12:06, 14 June 2023

Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex

Structural highlights

5chl is a 2 chain structure with sequence from Drosophila melanogaster and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VPS72_DROME Part of the Tip60 chromatin-remodeling complex which is involved in DNA repair. Upon induction of DNA double-strand breaks, this complex acetylates phosphorylated H2AV in nucleosomes and exchanges it with unmodified H2AV.^[1] ^[2]

Publication Abstract from PubMed

Histone variant H2A.Z, a universal mark of dynamic nucleosomes flanking gene promoters and enhancers, is incorporated into chromatin by SRCAP (SWR1), an ATP-dependent, multicomponent chromatin-remodeling complex. The YL1 (Swc2) subunit of SRCAP (SWR1) plays an essential role in H2A.Z recognition, but how it achieves this has been unclear. Here, we report the crystal structure of the H2A.Z-binding domain of Drosophila melanogaster YL1 (dYL1-Z) in complex with an H2A.Z-H2B dimer at 1.9-A resolution. The dYL1-Z domain adopts a new whip-like structure that wraps over H2A.Z-H2B, and preferential recognition is largely conferred by three residues in loop 2, the hyperacidic patch and the extended alphaC helix of H2A.Z. Importantly, this domain is essential for deposition of budding yeast H2A.Z in vivo and SRCAP (SWR1)-catalyzed histone H2A.Z replacement in vitro. Our studies distinguish YL1-Z from known H2A.Z chaperones and suggest a hierarchical mechanism based on increasing binding affinity facilitating H2A.Z transfer from SRCAP (SWR1) to the nucleosome.

Structural basis of H2A.Z recognition by SRCAP chromatin-remodeling subunit YL1.,Liang X, Shan S, Pan L, Zhao J, Ranjan A, Wang F, Zhang Z, Huang Y, Feng H, Wei D, Huang L, Liu X, Zhong Q, Lou J, Li G, Wu C, Zhou Z Nat Struct Mol Biol. 2016 Apr;23(4):317-23. doi: 10.1038/nsmb.3190. Epub 2016 Mar, 14. PMID:26974124^[3]

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

References

↑ Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science. 2004 Dec 17;306(5704):2084-7. Epub 2004 Nov 4. PMID:15528408 doi:https://dx.doi.org/1103455
↑ Wu WH, Alami S, Luk E, Wu CH, Sen S, Mizuguchi G, Wei D, Wu C. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol. 2005 Dec;12(12):1064-71. Epub 2005 Nov 20. PMID:16299513 doi:https://dx.doi.org/nsmb1023
↑ Liang X, Shan S, Pan L, Zhao J, Ranjan A, Wang F, Zhang Z, Huang Y, Feng H, Wei D, Huang L, Liu X, Zhong Q, Lou J, Li G, Wu C, Zhou Z. Structural basis of H2A.Z recognition by SRCAP chromatin-remodeling subunit YL1. Nat Struct Mol Biol. 2016 Apr;23(4):317-23. doi: 10.1038/nsmb.3190. Epub 2016 Mar, 14. PMID:26974124 doi:https://dx.doi.org/10.1038/nsmb.3190

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OCA

[1] Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science. 2004 Dec 17;306(5704):2084-7. Epub 2004 Nov 4. PMID:15528408 doi:https://dx.doi.org/1103455

[2] Wu WH, Alami S, Luk E, Wu CH, Sen S, Mizuguchi G, Wei D, Wu C. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol. 2005 Dec;12(12):1064-71. Epub 2005 Nov 20. PMID:16299513 doi:https://dx.doi.org/nsmb1023

[3] Liang X, Shan S, Pan L, Zhao J, Ranjan A, Wang F, Zhang Z, Huang Y, Feng H, Wei D, Huang L, Liu X, Zhong Q, Lou J, Li G, Wu C, Zhou Z. Structural basis of H2A.Z recognition by SRCAP chromatin-remodeling subunit YL1. Nat Struct Mol Biol. 2016 Apr;23(4):317-23. doi: 10.1038/nsmb.3190. Epub 2016 Mar, 14. PMID:26974124 doi:https://dx.doi.org/10.1038/nsmb.3190

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[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='5chl' size='340' side='right'caption='[[5chl]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5chl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CHL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5chl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CHL FirstGlance]. <br>
-</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=5chl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chl OCA], [http://pdbe.org/5chl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5chl RCSB], [http://www.ebi.ac.uk/pdbsum/5chl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5chl ProSAT]</span></td></tr>
+</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=5chl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chl OCA], [https://pdbe.org/5chl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5chl RCSB], [https://www.ebi.ac.uk/pdbsum/5chl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5chl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VPS72_DROME VPS72_DROME]] Part of the Tip60 chromatin-remodeling complex which is involved in DNA repair. Upon induction of DNA double-strand breaks, this complex acetylates phosphorylated H2AV in nucleosomes and exchanges it with unmodified H2AV.<ref>PMID:15528408</ref> <ref>PMID:16299513</ref>  [[http://www.uniprot.org/uniprot/H2AZ_HUMAN H2AZ_HUMAN]] Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. 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. May be involved in the formation of constitutive heterochromatin. May be required for chromosome segregation during cell division.<ref>PMID:15878876</ref>
+[https://www.uniprot.org/uniprot/VPS72_DROME VPS72_DROME] Part of the Tip60 chromatin-remodeling complex which is involved in DNA repair. Upon induction of DNA double-strand breaks, this complex acetylates phosphorylated H2AV in nucleosomes and exchanges it with unmodified H2AV.<ref>PMID:15528408</ref> <ref>PMID:16299513</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Drosophila melanogaster]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Liang, X]]
+[[Category: Liang X]]
-[[Category: Pan, L]]
+[[Category: Pan L]]
-[[Category: Shan, S]]
+[[Category: Shan S]]
-[[Category: Wu, C]]
+[[Category: Wu C]]
-[[Category: Zhou, Z]]
+[[Category: Zhou Z]]
-[[Category: Chaperone]]
-[[Category: Histone]]
-[[Category: Remodeling complex]]

5chl: Difference between revisions

Revision as of 12:06, 14 June 2023

Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex

Structural highlights

Function

Publication Abstract from PubMed

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References

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