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1KX5
Asym. Unit
Info
Asym.Unit (348 KB)
Biol.Unit 1 (338 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP147, AT 1.9 A RESOLUTION
Authors
:
C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, T. J. Richmond
Date
:
31 Jan 02 (Deposition) - 25 Dec 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
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, Chromatin, Histone, Protein-Dna Interaction, Nucleoprotein, Supercoiled Dna, Nucleosome Core, Protein- Dna Complex, Dna Bending, Dna Curvature, Dna-Cation Binding, Dna-Metal Binding, Dna Solvation, Structural Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, T. J. Richmond
Solvent Mediated Interactions In The Structure Of The Nucleosome Core Particle At 1. 9 A Resolution
J. Mol. Biol. V. 319 1097 2002
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MN
14
Ligand/Ion
MANGANESE (II) ION
[
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]
Sites
(18, 18)
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)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DG J:61 , HOH J:3221 , HOH J:3274 , HOH J:3430 , HOH J:3656 , HOH J:3694
BINDING SITE FOR RESIDUE MN J 3131
02
AC2
SOFTWARE
VAL D:45 , ASP E:77 , HOH E:3195 , HOH E:3214 , HOH E:3225 , HOH F:154
BINDING SITE FOR RESIDUE MN E 3132
03
AC3
SOFTWARE
HOH I:3158 , HOH I:3221 , DG J:27 , HOH J:3208 , HOH J:3209 , HOH J:3262
BINDING SITE FOR RESIDUE MN J 3133
04
AC4
SOFTWARE
DG J:-3 , HOH J:3169 , HOH J:3195 , HOH J:3226 , HOH J:3307 , HOH J:3917
BINDING SITE FOR RESIDUE MN J 3134
05
AC5
SOFTWARE
DG J:48 , HOH J:3201 , HOH J:3211 , HOH J:3316 , HOH J:3317
BINDING SITE FOR RESIDUE MN J 3135
06
AC6
SOFTWARE
HOH I:3212 , HOH I:3244 , HOH I:3261 , HOH I:3771 , HOH J:3175 , HOH J:3212
BINDING SITE FOR RESIDUE MN I 3136
07
AC7
SOFTWARE
DG I:48 , HOH I:3193 , HOH I:3209 , HOH I:3251 , HOH I:3306
BINDING SITE FOR RESIDUE MN I 3137
08
AC8
SOFTWARE
DG I:61 , HOH I:3152 , HOH I:3181 , HOH I:3201 , HOH I:3911
BINDING SITE FOR RESIDUE MN I 3138
09
AC9
SOFTWARE
DG J:-34 , DG J:-35 , HOH J:3215 , HOH J:3238 , HOH J:3331
BINDING SITE FOR RESIDUE MN J 3139
10
BC1
SOFTWARE
DG I:27 , HOH I:3243 , HOH I:3259 , HOH J:3931
BINDING SITE FOR RESIDUE MN I 3140
11
BC2
SOFTWARE
DG I:5 , HOH I:3204 , HOH J:3152 , HOH J:3240
BINDING SITE FOR RESIDUE MN I 3141
12
BC3
SOFTWARE
DG I:-3 , DG I:-2 , HOH I:3194 , HOH I:3333
BINDING SITE FOR RESIDUE MN I 3142
13
BC4
SOFTWARE
DG I:-35 , DG I:-34 , HOH I:3217 , HOH I:3232 , HOH I:3319 , HOH J:3933
BINDING SITE FOR RESIDUE MN I 3143
14
BC5
SOFTWARE
HOH I:3396 , HOH I:3923 , DG J:5 , HOH J:3230 , HOH J:3672
BINDING SITE FOR RESIDUE MN J 3144
15
BC6
SOFTWARE
GLY G:44 , GLY G:46 , ALA G:47 , THR H:87 , SER H:88
BINDING SITE FOR RESIDUE CL H 3145
16
BC7
SOFTWARE
GLY C:44 , GLY C:46 , ALA C:47 , THR D:87 , SER D:88
BINDING SITE FOR RESIDUE CL D 3146
17
BC8
SOFTWARE
PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 3147
18
BC9
SOFTWARE
PRO E:121 , LYS E:122
BINDING SITE FOR RESIDUE CL E 3148
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036206 (E63Q, chain B/F, )
2: VAR_H3_DROHY_001 (S96C, chain A/E, )
3: VAR_H3_DROHY_002 (I112M, chain A/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036206
E
64
Q
H4_HUMAN
Unclassified
---
B/F
E
63
Q
2
UniProt
VAR_H3_DROHY_001
*
S
97
C
H3_DROHY
---
---
A/E
S
96
C
3
UniProt
VAR_H3_DROHY_002
*
I
113
M
H3_DROHY
---
---
A/E
I
112
M
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 10)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H3_1 (A:14-20,E:14-20,A:14-20,E:14-20,A:...)
2: HISTONE_H4 (B:14-18,F:14-18,B:14-18,F:14-18,B:...)
3: HISTONE_H2A (C:21-27,G:21-27)
4: HISTONE_H3_2 (A:66-74,E:66-74,A:66-74,E:66-74,A:...)
5: HISTONE_H2B (D:89-111,H:89-111)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H3_1
PS00322
Histone H3 signature 1.
H32_BOVIN
15-21
2
A:14-20
E:14-20
H32_CAIMO
15-21
2
A:14-20
E:14-20
H32_CHICK
15-21
2
A:14-20
E:14-20
H3_CHITH
15-21
2
A:14-20
E:14-20
H3_DROHY
15-21
2
A:14-20
E:14-20
H3_PLADU
15-21
2
A:14-20
E:14-20
H3_TIGCA
15-21
2
A:14-20
E:14-20
H3_URECA
15-21
2
A:14-20
E:14-20
H32_ICTBU
15-21
2
A:14-20
E:14-20
H32_MOUSE
15-21
2
A:14-20
E:14-20
H32_ONCMY
15-21
2
A:14-20
E:14-20
H32_PORAF
15-21
2
A:14-20
E:14-20
H32_XENLA
15-21
2
A:14-20
E:14-20
2
HISTONE_H4
PS00047
Histone H4 signature.
H4_BOVIN
15-19
2
B:14-18
F:14-18
H4_CAIMO
15-19
2
B:14-18
F:14-18
H4_CHICK
15-19
2
B:14-18
F:14-18
H4_HUMAN
15-19
2
B:14-18
F:14-18
H4_MOUSE
15-19
2
B:14-18
F:14-18
H4_ONCMY
15-19
2
B:14-18
F:14-18
H4_ORENI
15-19
2
B:14-18
F:14-18
H4_PIG
15-19
2
B:14-18
F:14-18
H4_PLADU
15-19
2
B:14-18
F:14-18
H4_RAT
15-19
2
B:14-18
F:14-18
H4_URECA
15-19
2
B:14-18
F:14-18
H4_XENBO
15-19
2
B:14-18
F:14-18
H4_XENLA
15-19
2
B:14-18
F:14-18
3
HISTONE_H2A
PS00046
Histone H2A signature.
H2A1_XENLA
22-28
2
C:21-27
G:21-27
4
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H32_BOVIN
67-75
2
A:66-74
E:66-74
H32_CAIMO
67-75
2
A:66-74
E:66-74
H32_CHICK
67-75
2
A:66-74
E:66-74
H3_CHITH
67-75
2
A:66-74
E:66-74
H3_DROHY
67-75
2
A:66-74
E:66-74
H3_PLADU
67-75
2
A:66-74
E:66-74
H3_TIGCA
67-75
2
A:66-74
E:66-74
H3_URECA
67-75
2
A:66-74
E:66-74
H32_ICTBU
67-75
2
A:66-74
E:66-74
H32_MOUSE
67-75
2
A:66-74
E:66-74
H32_ONCMY
67-75
2
A:66-74
E:66-74
H32_PORAF
67-75
2
A:66-74
E:66-74
H32_XENLA
67-75
2
A:66-74
E:66-74
5
HISTONE_H2B
PS00357
Histone H2B signature.
H2B11_XENLA
93-115
2
D:89-111
H:89-111
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1kx5c_ (C:)
1b: SCOP_d1kx5g_ (G:)
2a: SCOP_d1kx5d_ (D:)
2b: SCOP_d1kx5h_ (H:)
3a: SCOP_d1kx5a_ (A:)
3b: SCOP_d1kx5e_ (E:)
4a: SCOP_d1kx5b_ (B:)
4b: SCOP_d1kx5f_ (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)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(34)
1a
d1kx5c_
C:
1b
d1kx5g_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d1kx5d_
D:
2b
d1kx5h_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d1kx5a_
A:
3b
d1kx5e_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d1kx5b_
B:
4b
d1kx5f_
F:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1kx5B00 (B:1-102)
1b: CATH_1kx5C00 (C:1-128)
1c: CATH_1kx5G00 (G:1-128)
1d: CATH_1kx5D00 (D:1-122)
1e: CATH_1kx5H00 (H:1-122)
1f: CATH_1kx5A00 (A:1-135)
1g: CATH_1kx5E00 (E:1-135)
1h: CATH_1kx5F00 (F:1-102)
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(
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Homologous Superfamilies
(
)
(
)
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
1kx5B00
B:1-102
1b
1kx5C00
C:1-128
1c
1kx5G00
G:1-128
1d
1kx5D00
D:1-122
1e
1kx5H00
H:1-122
1f
1kx5A00
A:1-135
1g
1kx5E00
E:1-135
1h
1kx5F00
F:1-102
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_1kx5G01 (G:17-90)
1b: PFAM_Histone_1kx5G02 (G:17-90)
1c: PFAM_Histone_1kx5H01 (H:28-98)
1d: PFAM_Histone_1kx5H02 (H:28-98)
1e: PFAM_Histone_1kx5E01 (E:57-131)
1f: PFAM_Histone_1kx5E02 (E:57-131)
1g: PFAM_Histone_1kx5F01 (F:24-93)
1h: PFAM_Histone_1kx5F02 (F:24-93)
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Clans
(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Histone
(49)
Family
:
Histone
(46)
Xenopus laevis (African clawed frog)
(32)
1a
Histone-1kx5G01
G:17-90
1b
Histone-1kx5G02
G:17-90
1c
Histone-1kx5H01
H:28-98
1d
Histone-1kx5H02
H:28-98
1e
Histone-1kx5E01
E:57-131
1f
Histone-1kx5E02
E:57-131
1g
Histone-1kx5F01
F:24-93
1h
Histone-1kx5F02
F:24-93
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Asym.Unit (348 KB)
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