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98 a.a.
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79 a.a.
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107 a.a.
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91 a.a.
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81 a.a.
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* Residue conservation analysis
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PDB id:
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Structural protein/DNA
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Title:
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Crystallographic studies of nucleosome core particles containing histone 'sin' mutants
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Structure:
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Palindromic 146bp human alpha-satellite DNA fragment. Chain: i, j. Engineered: yes. Histone h3. Chain: a, e. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: hb 101. Xenopus laevis. African clawed frog. Organism_taxid: 8355.
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Biol. unit:
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Decamer (from
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Resolution:
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3.00Å
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R-factor:
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0.203
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R-free:
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0.260
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Authors:
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U.M.Muthurajan,Y.Bao,L.J.Forsberg,R.S.Edayathumangalam,P.N.Dyer, C.L.White,K.Luger
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Key ref:
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U.M.Muthurajan
et al.
(2004).
Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions.
EMBO J,
23,
260-271.
PubMed id:
DOI:
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Date:
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17-Apr-03
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Release date:
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24-Feb-04
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PROCHECK
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Headers
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References
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P84233
(H32_XENLA) -
Histone H3.2 from Xenopus laevis
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Seq:
Struc:
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136 a.a.
98 a.a.*
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P62799
(H4_XENLA) -
Histone H4 from Xenopus laevis
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Seq:
Struc:
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103 a.a.
79 a.a.
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P06897
(H2A1_XENLA) -
Histone H2A type 1 from Xenopus laevis
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Seq:
Struc:
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130 a.a.
107 a.a.*
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DOI no:
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EMBO J
23:260-271
(2004)
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PubMed id:
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Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions.
|
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U.M.Muthurajan,
Y.Bao,
L.J.Forsberg,
R.S.Edayathumangalam,
P.N.Dyer,
C.L.White,
K.Luger.
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ABSTRACT
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Here we describe 11 crystal structures of nucleosome core particles containing
individual point mutations in the structured regions of histones H3 and H4. The
mutated residues are located at the two protein-DNA interfaces flanking the
nucleosomal dyad. Five of the mutations partially restore the in vivo effects of
SWI/SNF inactivation in yeast. We find that even nonconservative mutations of
these residues (which exhibit a distinct phenotype in vivo) have only moderate
effects on global nucleosome structure. Rather, local protein-DNA interactions
are disrupted and weakened in a subtle and complex manner. The number of lost
protein-DNA interactions correlates directly with an increased propensity of the
histone octamer to reposition with respect to the DNA, and with an overall
destabilization of the nucleosome. Thus, the disruption of only two to six of
the approximately 120 direct histone-DNA interactions within the nucleosome has
a pronounced effect on nucleosome mobility and stability. This has implications
for our understanding of how these structures are made accessible to the
transcription and replication machinery in vivo.
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Selected figure(s)
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Figure 1.
Figure 1 Location and structural context of histone Sin mutants.
(A) Overview of the NCP structure, viewed down the superhelical
axis. Only half of the DNA and associated proteins are shown.
SHLs are indicated by italic numbers from 0.5 (flanking the
nucleosomal dyad) to 6.5 (at the entry and exit point of the
DNA). The locations of the H4 L1 loop and the H3 L2 loop are
indicated in green and blue, respectively. Histone H3 is colored
in blue, H4 in green, H2A in yellow, and H2B in red. The box
indicates the location of Sin mutants. The nucleosomal dyad is
indicated (  ).
(B) Close-up of the Sin region showing the five residues
affected by Sin mutations. Dotted lines represent hydrogen
bonds. (C) Location of H4 Val-43 in the hydrophobic core at the
underside of the L1L2 loop arrangement. The view is similar as
in (B), with a slight rotation around the y-axis.
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Figure 5.
Figure 5 Changed solvent structure in H3 Arg-116 mutants. (A)
The 'van der Waals cup' formed by H3 Met-120, Pro-121, and
Lys-122, holding the chloride ion. 2Fo-Fc electron density,
contoured at 1 sigma, is shown in gold. (B) The same region is
shown for H3 Arg-116-His (blue). Note the missing density for
the chloride ion. (C) In H3 Arg-116-Ala, minor density is
observed for the chloride ion, indicating only partial
occupancy. (D) Superposition of the three structures, viewed
from above with respect to the views shown in (A -C). Wild type
is shown in wheat, and mutants in blue. The chloride ion is
omitted for clarity.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2004,
23,
260-271)
copyright 2004.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
|
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Reference
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A.J.Andrews,
and
K.Luger
(2011).
Nucleosome structure(s) and stability: variations on a theme.
|
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Annu Rev Biophys,
40,
99.
|
|
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|
|
|
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A.Marathe,
and
M.Bansal
(2011).
An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression.
|
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BMC Struct Biol,
11,
1.
|
|
|
|
|
|
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S.Ramachandran,
L.Vogel,
B.D.Strahl,
and
N.V.Dokholyan
(2011).
Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation.
|
| |
PLoS Comput Biol,
7,
e1001042.
|
|
|
|
|
|
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S.Tan,
and
C.A.Davey
(2011).
Nucleosome structural studies.
|
| |
Curr Opin Struct Biol,
21,
128-136.
|
|
|
|
|
|
|
A.Bowman,
R.Ward,
H.El-Mkami,
T.Owen-Hughes,
and
D.G.Norman
(2010).
Probing the (H3-H4)2 histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling.
|
| |
Nucleic Acids Res,
38,
695-707.
|
|
|
|
|
|
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F.K.Hsieh,
M.Fisher,
A.Ujvári,
V.M.Studitsky,
and
D.S.Luse
(2010).
Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II.
|
| |
EMBO Rep,
11,
705-710.
|
|
|
|
|
|
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F.Xu,
A.V.Colasanti,
Y.Li,
and
W.K.Olson
(2010).
Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures.
|
| |
Nucleic Acids Res,
38,
6872-6882.
|
|
|
|
|
|
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G.D.Bowman
(2010).
Mechanisms of ATP-dependent nucleosome sliding.
|
| |
Curr Opin Struct Biol,
20,
73-81.
|
|
|
|
|
|
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H.Tachiwana,
W.Kagawa,
A.Osakabe,
K.Kawaguchi,
T.Shiga,
Y.Hayashi-Takanaka,
H.Kimura,
and
H.Kurumizaka
(2010).
Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T.
|
| |
Proc Natl Acad Sci U S A,
107,
10454-10459.
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PDB codes:
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M.A.Hall,
A.Shundrovsky,
L.Bai,
R.M.Fulbright,
J.T.Lis,
and
M.D.Wang
(2009).
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.
|
| |
Nat Struct Mol Biol,
16,
124-129.
|
|
|
|
|
|
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M.Manohar,
A.M.Mooney,
J.A.North,
R.J.Nakkula,
J.W.Picking,
A.Edon,
R.Fishel,
M.G.Poirier,
and
J.J.Ottesen
(2009).
Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding.
|
| |
J Biol Chem,
284,
23312-23321.
|
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|
|
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|
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M.Sakamoto,
S.Noguchi,
S.Kawashima,
Y.Okada,
T.Enomoto,
M.Seki,
and
M.Horikoshi
(2009).
Global analysis of mutual interaction surfaces of nucleosomes with comprehensive point mutants.
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| |
Genes Cells,
14,
1271-1330.
|
|
|
|
|
|
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N.B.Becker,
and
R.Everaers
(2009).
DNA nanomechanics in the nucleosome.
|
| |
Structure,
17,
579-589.
|
|
|
|
|
|
|
S.Balasubramanian,
F.Xu,
and
W.K.Olson
(2009).
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
|
| |
Biophys J,
96,
2245-2260.
|
|
|
|
|
|
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S.Javaid,
M.Manohar,
N.Punja,
A.Mooney,
J.J.Ottesen,
M.G.Poirier,
and
R.Fishel
(2009).
Nucleosome remodeling by hMSH2-hMSH6.
|
| |
Mol Cell,
36,
1086-1094.
|
|
|
|
|
|
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V.R.Ramirez-Carrozzi,
D.Braas,
D.M.Bhatt,
C.S.Cheng,
C.Hong,
K.R.Doty,
J.C.Black,
A.Hoffmann,
M.Carey,
and
S.T.Smale
(2009).
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.
|
| |
Cell,
138,
114-128.
|
|
|
|
|
|
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A.Bende,
F.Bogár,
F.Beleznay,
and
J.Ladik
(2008).
Calculation of the hole mobilities of the three homopolynucleotides, poly(guanilic acid), poly(adenilic acid), and polythymidine in the presence of water and Na+ ions.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
78,
061923.
|
|
|
|
|
|
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D.Svozil,
J.Kalina,
M.Omelka,
and
B.Schneider
(2008).
DNA conformations and their sequence preferences.
|
| |
Nucleic Acids Res,
36,
3690-3706.
|
|
|
|
|
|
|
H.N.Du,
I.M.Fingerman,
and
S.D.Briggs
(2008).
Histone H3 K36 methylation is mediated by a trans-histone methylation pathway involving an interaction between Set2 and histone H4.
|
| |
Genes Dev,
22,
2786-2798.
|
|
|
|
|
|
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H.Tachiwana,
A.Osakabe,
H.Kimura,
and
H.Kurumizaka
(2008).
Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.
|
| |
Nucleic Acids Res,
36,
2208-2218.
|
|
|
|
|
|
|
J.Ladik,
A.Bende,
and
F.Bogár
(2008).
The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water.
|
| |
J Chem Phys,
128,
105101.
|
|
|
|
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|
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Q.He,
C.Yu,
and
R.H.Morse
(2008).
Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae.
|
| |
Eukaryot Cell,
7,
1649-1660.
|
|
|
|
|
|
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R.Nag,
F.Gong,
D.Fahy,
and
M.J.Smerdon
(2008).
A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast.
|
| |
Nucleic Acids Res,
36,
3857-3866.
|
|
|
|
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|
|
S.Nakanishi,
B.W.Sanderson,
K.M.Delventhal,
W.D.Bradford,
K.Staehling-Hampton,
and
A.Shilatifard
(2008).
A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation.
|
| |
Nat Struct Mol Biol,
15,
881-888.
|
|
|
|
|
|
|
T.C.Bishop
(2008).
Geometry of the nucleosomal DNA superhelix.
|
| |
Biophys J,
95,
1007-1017.
|
|
|
|
|
|
|
H.Ferreira,
J.Somers,
R.Webster,
A.Flaus,
and
T.Owen-Hughes
(2007).
Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability.
|
| |
Mol Cell Biol,
27,
4037-4048.
|
|
|
|
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|
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K.Matsubara,
N.Sano,
T.Umehara,
and
M.Horikoshi
(2007).
Global analysis of functional surfaces of core histones with comprehensive point mutants.
|
| |
Genes Cells,
12,
13-33.
|
|
|
|
|
|
|
M.S.Cosgrove
(2007).
Histone proteomics and the epigenetic regulation of nucleosome mobility.
|
| |
Expert Rev Proteomics,
4,
465-478.
|
|
|
|
|
|
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S.A.Danziger,
J.Zeng,
Y.Wang,
R.K.Brachmann,
and
R.H.Lathrop
(2007).
Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants.
|
| |
Bioinformatics,
23,
i104-i114.
|
|
|
|
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|
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C.J.Fry,
A.Norris,
M.Cosgrove,
J.D.Boeke,
and
C.L.Peterson
(2006).
The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing.
|
| |
Mol Cell Biol,
26,
9045-9059.
|
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|
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|
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C.L.Woodcock
(2006).
Chromatin architecture.
|
| |
Curr Opin Struct Biol,
16,
213-220.
|
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|
|
|
|
|
E.L.Mersfelder,
and
M.R.Parthun
(2006).
The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure.
|
| |
Nucleic Acids Res,
34,
2653-2662.
|
|
|
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|
|
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K.Luger
(2006).
Dynamic nucleosomes.
|
| |
Chromosome Res,
14,
5.
|
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|
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M.K.Gilbert,
Y.Y.Tan,
and
C.M.Hart
(2006).
The Drosophila boundary element-associated factors BEAF-32A and BEAF-32B affect chromatin structure.
|
| |
Genetics,
173,
1365-1375.
|
|
|
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S.Chakravarthy,
and
K.Luger
(2006).
The histone variant macro-H2A preferentially forms "hybrid nucleosomes".
|
| |
J Biol Chem,
281,
25522-25531.
|
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|
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S.Jimeno-González,
F.Gómez-Herreros,
P.M.Alepuz,
and
S.Chávez
(2006).
A gene-specific requirement for FACT during transcription is related to the chromatin organization of the transcribed region.
|
| |
Mol Cell Biol,
26,
8710-8721.
|
|
|
|
|
|
|
E.M.Hyland,
M.S.Cosgrove,
H.Molina,
D.Wang,
A.Pandey,
R.J.Cottee,
and
J.D.Boeke
(2005).
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae.
|
| |
Mol Cell Biol,
25,
10060-10070.
|
|
|
|
|
|
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L.Mariño-Ramírez,
M.G.Kann,
B.A.Shoemaker,
and
D.Landsman
(2005).
Histone structure and nucleosome stability.
|
| |
Expert Rev Proteomics,
2,
719-729.
|
|
|
|
|
|
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M.S.Cosgrove,
and
C.Wolberger
(2005).
How does the histone code work?
|
| |
Biochem Cell Biol,
83,
468-476.
|
|
|
|
|
|
|
A.Flaus,
and
T.Owen-Hughes
(2004).
Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?
|
| |
Curr Opin Genet Dev,
14,
165-173.
|
|
|
|
|
|
|
M.S.Cosgrove,
J.D.Boeke,
and
C.Wolberger
(2004).
Regulated nucleosome mobility and the histone code.
|
| |
Nat Struct Mol Biol,
11,
1037-1043.
|
|
|
|
|
|
|
Y.Bao,
K.Konesky,
Y.J.Park,
S.Rosu,
P.N.Dyer,
D.Rangasamy,
D.J.Tremethick,
P.J.Laybourn,
and
K.Luger
(2004).
Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA.
|
| |
EMBO J,
23,
3314-3324.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
