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2CV5
Asym. Unit
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Asym.Unit (254 KB)
Biol.Unit 1 (249 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN NUCLEOSOME CORE PARTICLE
Authors
:
Y. Tsunaka, N. Kajimura, S. Tate, K. Morikawa
Date
:
31 May 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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
:
Human Nucleosome Structure, X-Ray Crystallography, Supercoiled Dna Path, Metal Binding Site, Structural Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Tsunaka, N. Kajimura, S. Tate, K. Morikawa
Alteration Of The Nucleosomal Dna Path In The Crystal Structure Of A Human Nucleosome Core Particle
Nucleic Acids Res. V. 33 3424 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 13)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MN
9
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DG J:185 , DG J:186 , HOH J:1043 , HOH J:1046
BINDING SITE FOR RESIDUE MN J 1001
02
AC2
SOFTWARE
DG J:267 , HOH J:1041 , HOH J:1044 , HOH J:1071
BINDING SITE FOR RESIDUE MN J 1002
03
AC3
SOFTWARE
DG J:217 , HOH J:1042
BINDING SITE FOR RESIDUE MN J 1003
04
AC4
SOFTWARE
DG I:68 , HOH I:1039 , HOH J:1081
BINDING SITE FOR RESIDUE MN I 1004
05
AC5
SOFTWARE
DG I:121
BINDING SITE FOR RESIDUE MN I 1005
06
AC6
SOFTWARE
DG J:280
BINDING SITE FOR RESIDUE MN J 1006
07
AC7
SOFTWARE
DG I:134 , HOH I:1042
BINDING SITE FOR RESIDUE MN I 1007
08
AC8
SOFTWARE
VAL D:45 , HOH D:1026 , ASP E:77 , HOH E:2048
BINDING SITE FOR RESIDUE MN D 1008
09
AC9
SOFTWARE
HOH I:1095 , HOH J:1087 , HOH J:1088
BINDING SITE FOR RESIDUE MN J 1009
10
BC1
SOFTWARE
GLY C:46 , ALA C:47 , THR D:87 , SER D:88
BINDING SITE FOR RESIDUE CL C 2001
11
BC2
SOFTWARE
GLY G:44 , ALA G:45 , GLY G:46 , ALA G:47 , THR H:87 , SER H:88
BINDING SITE FOR RESIDUE CL G 2002
12
BC3
SOFTWARE
PRO E:121 , LYS E:122
BINDING SITE FOR RESIDUE CL E 2003
13
BC4
SOFTWARE
PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 2004
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036206 (E63Q, chain B/F, )
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
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:21-27,G:21-27)
2: HISTONE_H3_2 (A:66-74,E:66-74)
3: 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_H2A
PS00046
Histone H2A signature.
H2A1B_HUMAN
22-28
2
C:21-27
G:21-27
2
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H31_HUMAN
67-75
2
A:66-74
E:66-74
3
HISTONE_H2B
PS00357
Histone H2B signature.
H2B1K_HUMAN
93-115
2
D:89-111
H:89-111
[
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Exons
(3, 6)
Info
All Exons
Exon 1.1b (D:27-122 | H:28-121)
Exon 2.2b (A:38-134 | E:37-135)
Exon 3.1 (B:25-102 | F:18-102)
View:
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All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/-
3: Boundary -/2.2b
4: Boundary 2.2b/-
5: Boundary -/3.1
6: Boundary 3.1/-
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
1.1b
ENST00000356950
1b
ENSE00001986308
chr6:
27114577-27114197
381
H2B1K_HUMAN
1-126
126
2
D:27-122
H:28-121
96
94
2.2b
ENST00000359303
2b
ENSE00001974165
chr6:
27858570-27858160
411
H31_HUMAN
1-136
136
2
A:38-134
E:37-135
97
99
3.1
ENST00000377803
1
ENSE00001475159
chr6:
26104104-26104518
415
H4_HUMAN
1-127
127
2
B:25-102
F:18-102
78
85
[
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SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2cv5c1 (C:11-118)
1b: SCOP_d2cv5g_ (G:)
2a: SCOP_d2cv5d1 (D:27-122)
2b: SCOP_d2cv5h_ (H:)
3a: SCOP_d2cv5a_ (A:)
3b: SCOP_d2cv5e_ (E:)
4a: SCOP_d2cv5b_ (B:)
4b: SCOP_d2cv5f_ (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)
Human (Homo sapiens), H2A.a [TaxId: 9606]
(1)
1a
d2cv5c1
C:11-118
1b
d2cv5g_
G:
Protein domain
:
Histone H2B
(48)
Human (Homo sapiens), H2B.k [TaxId: 9606]
(1)
2a
d2cv5d1
D:27-122
2b
d2cv5h_
H:
Protein domain
:
Histone H3
(58)
Human (Homo sapiens) [TaxId: 9606]
(10)
3a
d2cv5a_
A:
3b
d2cv5e_
E:
Protein domain
:
Histone H4
(60)
Human (Homo sapiens) [TaxId: 9606]
(11)
4a
d2cv5b_
B:
4b
d2cv5f_
F:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2cv5A00 (A:38-134)
1b: CATH_2cv5E00 (E:37-135)
1c: CATH_2cv5D00 (D:27-122)
1d: CATH_2cv5H00 (H:28-121)
1e: CATH_2cv5F00 (F:18-102)
1f: CATH_2cv5G00 (G:15-118)
1g: CATH_2cv5C00 (C:11-118)
1h: CATH_2cv5B00 (B:25-102)
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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)
[unclassified]
(10)
1a
2cv5A00
A:38-134
1b
2cv5E00
E:37-135
1c
2cv5D00
D:27-122
1d
2cv5H00
H:28-121
1e
2cv5F00
F:18-102
1f
2cv5G00
G:15-118
1g
2cv5C00
C:11-118
1h
2cv5B00
B:25-102
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Chain H
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Chain J
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