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* Residue conservation analysis
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PDB id:
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Chaperone/structural protein
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Title:
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Crystal structure of the cia- histone h3-h4 complex
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Structure:
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Asf1a protein. Chain: a. Fragment: residues 1-172. Synonym: cia, ccg1-interacting factor a, anti silencing function 1 homolog a. Engineered: yes. Histone h3.1. Chain: b. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: asf1a. Expressed in: escherichia coli. Expression_system_taxid: 562. Xenopus laevis. African clawed frog. Organism_taxid: 8355.
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Resolution:
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2.70Å
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R-factor:
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0.240
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R-free:
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0.293
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Authors:
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R.Natsume,Y.Akai,M.Horikoshi,T.Senda
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Key ref:
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R.Natsume
et al.
(2007).
Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4.
Nature,
446,
338-341.
PubMed id:
DOI:
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Date:
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10-Oct-06
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Release date:
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27-Feb-07
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PROCHECK
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Headers
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References
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Q9Y294
(ASF1A_HUMAN) -
Histone chaperone ASF1A from Homo sapiens
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Seq:
Struc:
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204 a.a.
154 a.a.
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DOI no:
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Nature
446:338-341
(2007)
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PubMed id:
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Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4.
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R.Natsume,
M.Eitoku,
Y.Akai,
N.Sano,
M.Horikoshi,
T.Senda.
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ABSTRACT
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CIA (CCG1-interacting factor A)/ASF1, which is the most conserved histone
chaperone among the eukaryotes, was genetically identified as a factor for an
anti-silencing function (Asf1) by yeast genetic screening. Shortly after that,
the CIA-histone-H3-H4 complex was isolated from Drosophila as a histone
chaperone CAF-1 stimulator. Human CIA-I/II (ASF1a/b) was identified as a histone
chaperone that interacts with the bromodomain-an acetylated-histone-recognizing
domain-of CCG1, in the general transcription initiation factor TFIID. Intensive
studies have revealed that CIA/ASF1 mediates nucleosome assembly by forming a
complex with another histone chaperone in human cells and yeast, and is involved
in DNA replication, transcription, DNA repair and silencing/anti-silencing in
yeast. CIA/ASF1 was shown as a major storage chaperone for soluble histones in
proliferating human cells. Despite all these biochemical and biological
functional analyses, the structure-function relationship of the nucleosome
assembly/disassembly activity of CIA/ASF1 has remained elusive. Here we report
the crystal structure, at 2.7 A resolution, of CIA-I in complex with histones H3
and H4. The structure shows the histone H3-H4 dimer's mutually exclusive
interactions with another histone H3-H4 dimer and CIA-I. The carboxy-terminal
beta-strand of histone H4 changes its partner from the beta-strand in histone
H2A to that of CIA-I through large conformational change. In vitro functional
analysis demonstrated that CIA-I has a histone H3-H4 tetramer-disrupting
activity. Mutants with weak histone H3-H4 dimer binding activity showed critical
functional effects on cellular processes related to transcription. The histone
H3-H4 tetramer-disrupting activity of CIA/ASF1 and the crystal structure of the
CIA/ASF1-histone-H3-H4 dimer complex should give insights into mechanisms of
both nucleosome assembly/disassembly and nucleosome semi-conservative
replication.
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Selected figure(s)
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Figure 1.
Figure 1: Overall structure and biochemical analysis of the
CIA-I–histone-H3–H4 complex. a, The overall structure
of the CIA-I–histone-H3–H4 complex. CIA-I and histones H3
and H4 are shown in red, blue, and green, respectively. An
orange triangle indicates the HIRA (histone regulatory homologue
A) binding site^28. The molecular graphics were prepared by
PyMOL^29. b, Possible modification sites (stick model in orange)
and the different residues of human histone H3.1 and H3.3 in the
CIA-I–histone-H3–H4 complex (sphere model in pink, only
exposed residues are displayed). c, The histone H3–H3'
interaction in the nucleosome core^21. d, CIA-I–histone H3
interaction in the CIA-I–histone-H3–H4 complex. e,
Carboxy-terminal residues (Thr 96–Tyr 98) of histone H4
(green) form a parallel  -sheet
with a -strand
from H2A (yellow) in the nucleosome core^21. f, The C-terminal
fragment of histone H4 undergoes a conformational change on the
CIA-I–histone-H3–H4 complex formation through rotations of
main-chain  angles
of Gly 94 and Arg 95 by 95° and 75°, respectively.
Histone H4s in the present structure and the nucleosome
core are shown in green and light green, respectively. This
conformational change and formation of a new anti-parallel -sheet
might facilitate the histone H3–H4 tetramer-disruption. The
large effect (tetramer disruption) originating from a small
interaction (formation of -sheet)
is similar to the essence of Japanese Judo (Yawara): 'softness
tames toughness (ju yoku go wo seisu)'. Following the spirit of
Judo, we designated the mechanism as the 'Yawara split'. It is
intriguing to note that most histone chaperones have a -rich
structure. g, Pull-down assay with GST-tagged human CIA-I(155)
or GST (control), showing the stoichiometric interaction between
CIA and the histone H3–H4 complex. h, Determination of the
molecular weight of human CIA, histone dimer, tetramer, and
complexes by the static light-scattering method. LS and RI
represent the intensity of static light scattering and the
refractive index, respectively.
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Figure 3.
Figure 3: Physical and functional interaction between CIA and
histone H4. a, Interaction between the residues in the
secondary binding site (red) and histone H4 (green). b, The
hydrophobic pocket in the secondary binding site (red) of CIA-I
accommodates Phe 100(H4) (green). c, GST pull-down assay for
histone H3 and H4 mutants by GST-tagged human CIA-I(155).
The results of the densitometry are summarized in graphs c
and d. The error bars in the graphs represent standard
deviations. d, GST pull-down assay for histone H3 and H4 mutants
by GST-tagged yeast Asf1p/Cia1p(169).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
446,
338-341)
copyright 2007.
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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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Structural plasticity of histones H3-H4 facilitates their allosteric exchange between RbAp48 and ASF1.
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Nat Struct Mol Biol,
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PDB code:
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PDB code:
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PDB codes:
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G.C.Johnston,
R.A.Singer,
and
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PDB codes:
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U.Ohler,
and
D.A.Wassarman
(2010).
Promoting developmental transcription.
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Development,
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Y.Akai,
N.Adachi,
Y.Hayashi,
M.Eitoku,
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M.Tanokura,
T.Senda,
and
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Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction.
|
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Proc Natl Acad Sci U S A,
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PDB code:
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Y.Liu,
H.Huang,
B.O.Zhou,
S.S.Wang,
Y.Hu,
X.Li,
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J.Wu,
J.Q.Zhou,
M.Teng,
and
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Structural analysis of Rtt106p reveals a DNA binding role required for heterochromatin silencing.
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J Biol Chem,
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PDB codes:
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A.Groth
(2009).
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Proc Natl Acad Sci U S A,
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PDB code:
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PDB code:
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| |
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PDB codes:
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A.Galvani,
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In vivo study of the nucleosome assembly functions of ASF1 histone chaperones in human cells.
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Mol Cell Biol,
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C.E.Berndsen,
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J.M.Holton,
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J.L.Keck,
and
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(2008).
Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75.
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Nat Struct Mol Biol,
15,
948-956.
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PDB codes:
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J.Dai,
E.M.Hyland,
D.S.Yuan,
H.Huang,
J.S.Bader,
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Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.
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Cell,
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M.M.Jensen,
M.S.Christensen,
B.Bonven,
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Requirements for chromatin reassembly during transcriptional downregulation of a heat shock gene in Saccharomyces cerevisiae.
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FEBS J,
275,
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N.V.Murzina,
X.Y.Pei,
W.Zhang,
M.Sparkes,
J.Vicente-Garcia,
J.V.Pratap,
S.H.McLaughlin,
T.R.Ben-Shahar,
A.Verreault,
B.F.Luisi,
and
E.D.Laue
(2008).
Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46.
|
| |
Structure,
16,
1077-1085.
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PDB codes:
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Q.Li,
H.Zhou,
H.Wurtele,
B.Davies,
B.Horazdovsky,
A.Verreault,
and
Z.Zhang
(2008).
Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly.
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Cell,
134,
244-255.
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R.M.Finn,
K.Browne,
K.C.Hodgson,
and
J.Ausió
(2008).
sNASP, a histone H1-specific eukaryotic chaperone dimer that facilitates chromatin assembly.
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Biophys J,
95,
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S.Henikoff
(2008).
Nucleosome destabilization in the epigenetic regulation of gene expression.
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Nat Rev Genet,
9,
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T.Stuwe,
M.Hothorn,
E.Lejeune,
V.Rybin,
M.Bortfeld,
K.Scheffzek,
and
A.G.Ladurner
(2008).
The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module.
|
| |
Proc Natl Acad Sci U S A,
105,
8884-8889.
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PDB codes:
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|
|
Y.J.Park,
and
K.Luger
(2008).
Histone chaperones in nucleosome eviction and histone exchange.
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Curr Opin Struct Biol,
18,
282-289.
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Y.Munemasa,
T.Suzuki,
K.Aizawa,
S.Miyamoto,
Y.Imai,
T.Matsumura,
M.Horikoshi,
and
R.Nagai
(2008).
Promoter region-specific histone incorporation by the novel histone chaperone ANP32B and DNA-binding factor KLF5.
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Mol Cell Biol,
28,
1171-1181.
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Y.Takayama,
H.Sato,
S.Saitoh,
Y.Ogiyama,
F.Masuda,
and
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(2008).
Biphasic Incorporation of Centromeric Histone CENP-A in Fission Yeast.
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Mol Biol Cell,
19,
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Z.Zhou,
H.Feng,
D.F.Hansen,
H.Kato,
E.Luk,
D.I.Freedberg,
L.E.Kay,
C.Wu,
and
Y.Bai
(2008).
NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B.
|
| |
Nat Struct Mol Biol,
15,
868-869.
|
|
|
PDB code:
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|
A.Groth,
A.Corpet,
A.J.Cook,
D.Roche,
J.Bartek,
J.Lukas,
and
G.Almouzni
(2007).
Regulation of replication fork progression through histone supply and demand.
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Science,
318,
1928-1931.
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A.Loyola,
and
G.Almouzni
(2007).
Marking histone H3 variants: how, when and why?
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Trends Biochem Sci,
32,
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D.Ray-Gallet,
J.P.Quivy,
H.W.Silljé,
E.A.Nigg,
and
G.Almouzni
(2007).
The histone chaperone Asf1 is dispensable for direct de novo histone deposition in Xenopus egg extracts.
|
| |
Chromosoma,
116,
487-496.
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H.J.Kim,
J.H.Seol,
J.W.Han,
H.D.Youn,
and
E.J.Cho
(2007).
Histone chaperones regulate histone exchange during transcription.
|
| |
EMBO J,
26,
4467-4474.
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J.Han,
H.Zhou,
Z.Li,
R.M.Xu,
and
Z.Zhang
(2007).
Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity.
|
| |
J Biol Chem,
282,
28587-28596.
|
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|
|
L.De Koning,
A.Corpet,
J.E.Haber,
and
G.Almouzni
(2007).
Histone chaperones: an escort network regulating histone traffic.
|
| |
Nat Struct Mol Biol,
14,
997.
|
|
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|
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|
|
Y.Dalal,
T.Furuyama,
D.Vermaak,
and
S.Henikoff
(2007).
Structure, dynamics, and evolution of centromeric nucleosomes.
|
| |
Proc Natl Acad Sci U S A,
104,
15974-15981.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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