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Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (221 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
Authors
:
C. L. White, R. K. Suto, K. Luger
Date
:
03 Apr 01 (Deposition) - 28 Sep 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Nucleosome Core Particle, Chromatin, Histone, Protein/Dna Interaction, Nucleoprotein, Supercoiled Dna, Complex (Nucleosome Core/Dna), Structural Protein/Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
C. L. White, R. K. Suto, K. Luger
Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Changes In Internucleosome Interactions.
Embo J. V. 20 5207 2001
(for further references see the
PDB file header
)
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Hetero Components
(1, 17)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
1i: MANGANESE (II) ION (MNi)
1j: MANGANESE (II) ION (MNj)
1k: MANGANESE (II) ION (MNk)
1l: MANGANESE (II) ION (MNl)
1m: MANGANESE (II) ION (MNm)
1n: MANGANESE (II) ION (MNn)
1o: MANGANESE (II) ION (MNo)
1p: MANGANESE (II) ION (MNp)
1q: MANGANESE (II) ION (MNq)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
17
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY G:45 , SER G:46 , GLY G:47 , SER H:93 , ALA H:94
BINDING SITE FOR RESIDUE MN H 131
02
AC2
SOFTWARE
ARG C:89
BINDING SITE FOR RESIDUE MN C 132
03
AC3
SOFTWARE
DG J:267
BINDING SITE FOR RESIDUE MN J 103
04
AC4
SOFTWARE
DA I:133 , DG I:134
BINDING SITE FOR RESIDUE MN I 147
05
AC5
SOFTWARE
DG I:70
BINDING SITE FOR RESIDUE MN I 148
06
AC6
SOFTWARE
ASP G:91 , GLU G:93
BINDING SITE FOR RESIDUE MN G 132
07
AC7
SOFTWARE
DG I:121
BINDING SITE FOR RESIDUE MN I 149
08
AC8
SOFTWARE
DA J:279 , DG J:280
BINDING SITE FOR RESIDUE MN J 108
09
AC9
SOFTWARE
ARG E:49 , DT I:8
BINDING SITE FOR RESIDUE MN E 136
10
BC1
SOFTWARE
ASP C:91 , GLU C:93
BINDING SITE FOR RESIDUE MN C 133
11
BC2
SOFTWARE
DG J:216 , DG J:217
BINDING SITE FOR RESIDUE MN J 111
12
BC3
SOFTWARE
DG I:78 , DG J:214
BINDING SITE FOR RESIDUE MN I 150
13
BC4
SOFTWARE
ASP C:73 , DC J:168
BINDING SITE FOR RESIDUE MN J 113
14
BC5
SOFTWARE
DT I:45 , DG J:246
BINDING SITE FOR RESIDUE MN J 114
15
BC6
SOFTWARE
DT J:184 , DG J:185 , DG J:186
BINDING SITE FOR RESIDUE MN J 115
16
BC7
SOFTWARE
GLU D:108 , HIS D:112 , GLU G:65 , HIS H:52
BINDING SITE FOR RESIDUE MN D 131
17
BC8
SOFTWARE
DA J:202 , DA J:203
BINDING SITE FOR RESIDUE MN J 117
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:22-28,G:22-28)
2: HISTONE_H3_2 (A:66-74,E:66-74)
3: HISTONE_H2B (D:95-117,H:95-117)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H2A
PS00046
Histone H2A signature.
H2A1_YEAST
23-29
2
C:22-28
G:22-28
2
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H3_YEAST
67-75
2
A:66-74
E:66-74
3
HISTONE_H2B
PS00357
Histone H2B signature.
H2B2_YEAST
96-118
2
D:95-117
H:95-117
[
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]
Exons
(4, 8)
Info
All Exons
Exon 1.1 (D:36-128 | H:35-130)
Exon 2.1 (C:16-125 | G:13-120)
Exon 3.1 (B:24-102 | F:18-102)
Exon 4.1 (A:38-134 | E:38-134)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
5: Boundary -/3.1
6: Boundary 3.1/-
7: Boundary -/4.1
8: Boundary 4.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YBL002W
1
YBL002W.1
II:236495-236890
396
H2B2_YEAST
1-131
131
2
D:36-128
H:35-130
93
96
2.1
YDR225W
1
YDR225W.1
IV:915527-915925
399
H2A1_YEAST
1-132
132
2
C:16-125
G:13-120
110
108
3.1
YNL030W
1
YNL030W.1
XIV:576729-577040
312
H4_YEAST
1-103
103
2
B:24-102
F:18-102
79
85
4.1
YNL031C
1
YNL031C.1
XIV:576052-575642
411
H3_YEAST
1-136
136
2
A:38-134
E:38-134
97
97
[
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SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1id3c_ (C:)
1b: SCOP_d1id3g_ (G:)
2a: SCOP_d1id3d_ (D:)
2b: SCOP_d1id3h_ (H:)
3a: SCOP_d1id3a_ (A:)
3b: SCOP_d1id3e_ (E:)
4a: SCOP_d1id3b_ (B:)
4b: SCOP_d1id3f_ (F:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Histone-fold
(277)
Superfamily
:
Histone-fold
(277)
Family
:
Nucleosome core histones
(247)
Protein domain
:
Histone H2A
(45)
Baker's yeast (Saccharomyces cerevisiae), H2A.1 [TaxId: 4932]
(2)
1a
d1id3c_
C:
1b
d1id3g_
G:
Protein domain
:
Histone H2B
(48)
Baker's yeast (Saccharomyces cerevisiae), H2B.2 [TaxId: 4932]
(2)
2a
d1id3d_
D:
2b
d1id3h_
H:
Protein domain
:
Histone H3
(58)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
3a
d1id3a_
A:
3b
d1id3e_
E:
Protein domain
:
Histone H4
(60)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
4a
d1id3b_
B:
4b
d1id3f_
F:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1id3A00 (A:38-134)
1b: CATH_1id3G00 (G:13-120)
1c: CATH_1id3C00 (C:16-125)
1d: CATH_1id3F00 (F:18-102)
1e: CATH_1id3B00 (B:24-102)
1f: CATH_1id3E00 (E:38-134)
1g: CATH_1id3H00 (H:35-130)
1h: CATH_1id3D00 (D:36-128)
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(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Histone, subunit A
(62)
Homologous Superfamily
:
Histone, subunit A
(62)
Human (Homo sapiens)
(28)
1a
1id3A00
A:38-134
1b
1id3G00
G:13-120
1c
1id3C00
C:16-125
1d
1id3F00
F:18-102
1e
1id3B00
B:24-102
1f
1id3E00
E:38-134
1g
1id3H00
H:35-130
1h
1id3D00
D:36-128
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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