Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer

Proteins: Structure, Function and Genetics

Volumn 71, Issue 1, 2008, Pages 1-7

  Clapier, Cedric R ^a   Chakravarthy, Srinivas ^b   Petosa, Carlo ^a   Fernández Tornero, Carlos ^a,c   Luger, Karolin ^b   Müller, Christoph W ^a,c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (France)

^b Department of Environmental and Radiological Health Sciences   (United States)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Chromatin; Crystal structure; Drosophila; Nucleosome core particles; Protein DNA interaction

Indexed keywords

DIMER; DNA FRAGMENT; HISTONE H2A; HISTONE H2B; SATELLITE DNA; SOLVENT;

AMINO ACID SUBSTITUTION; ARTICLE; BASE PAIRING; COEVOLUTION; CRYSTAL STRUCTURE; DROSOPHILA MELANOGASTER; HYDROPHOBICITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN LOCALIZATION; SEQUENCE HOMOLOGY; SPECIES COMPARISON; STRUCTURE ANALYSIS; XENOPUS LAEVIS;

AMINO ACID SUBSTITUTION; AMINO ACIDS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; HISTONES; HUMANS; HYDROPHOBICITY; NUCLEOSOMES; SOLVENTS; XENOPUS PROTEINS;

DROSOPHILA MELANOGASTER; INVERTEBRATA; VERTEBRATA; XENOPUS LAEVIS;

EID: 40549121635     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21720     Document Type: Article

References (35)

1. Kornberg RD, Thomas JO. Chromatin structure; oligomers of the histones. Science 1974;184:865-868.
2. Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science 1974;184:868-871.
3. Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999;98:285-294.
4. Workman JL. Nucleosome displacement in transcription. Genes Dev 2006;20:2009-2017.
5. Becker PB, Horz W. ATP-dependent nucleosome remodeling. Annu Rev Biochem 2002;71:247-273.
6. Narlikar GJ, Fan HY, Kingston RE. Cooperation between complexes that regulate chromatin structure and transcription. Cell 2002;108:475-487.
7. Fischle W, Wang Y, Allis CD. Histone and chromatin cross-talk. Curr Opin Cell Biol 2003;15:172-183.
8. Khorasanizadeh S. The nucleosome: from genomic organization to genomic regulation. Cell 2004;116:259-272.
9. Boyer LA, Mathur D, Jaenisch R. Molecular control of pluripotency. Curr Opin Genet Dev 2006;16:455-462.
10. Lieberman PM. Chromatin regulation of virus infection. Trends Microbiol 2006;14:132-140.
11. Lund AH, van Lohuizen M. Epigenetics and cancer. Genes Dev 2004;18:2315-2335.
12. Finch JT, Lutter LC, Rhodes D, Brown RS, Rushton B, Levitt M, Klug A. Structure of nucleosome core particles of chromatin. Nature 1977;269:29-36.
13. Bentley GA, Lewit-Bentley A, Finch JT, Podjarny AD, Roth M. Crystal structure of the nucleosome core particle at 16 A resolution. J Mol Biol 1984;176:55-75.
14. Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature 1984;311:532-537.
15. Arents G, Burlingame RW, Wang B-C, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 Å resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci USA 1991;88:10148-10152.
16. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997;389:251-260.
17. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol 2002;319:1097-1113.
18. Davey CA, Richmond TJ. DNA-dependent divalent cation binding in the nucleosome core particle. Proc Natl Acad Sci USA 2002;99:11169-11174.
19. Richmond TJ, Davey CA. The structure of DNA in the nucleosome core. Nature 2003;423:145-150.
20. Suto RK, Clarkson MJ, Tremethick DJ, Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol 2000;7:1121-1124.
21. Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K. Structural characterization of the histone variant macroH2A. Mol Cell Biol 2005;25:7616-7624.
22. Harp JM, Hanson BL, Timm DE, Bunick GJ. Asymmetries in the nucleosome core particle at 2.5 Å resolution. Acta Crystallogr D Biol Crystallogr 2000;56:1513-1534.
23. White CL, Suto RK, Luger K. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Embo J 2001;20:5207-5218.
24. Tsunaka Y, Kajimura N, Tate S, Morikawa K. Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucleic Acids Res 2005;33:3424-3434.
25. Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol 2004;375:23-44.
26. Kabsch W Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 1993;26:795-800.
27. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
28. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
29. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
30. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. Embo J 1986;5:823-826.
31. Hubbard TJ, Blundell TL. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1987;1:159-171.
32. Flores TP, Orengo CA, Moss DS, Thornton JM. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993;2:1811-1826.
33. Russell RB, Saqi MA, Sayle RA, Bates PA, Sternberg MJ. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 1997;269:423-439.
34. Sullivan SA, Landsman D. Characterization of sequence variability in nucleosome core histone folds. Proteins 2003;52:454-465.
35. Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM. The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Science 2006;311:856-861.