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1EQZ
Biol. Unit 1
Info
Asym.Unit (277 KB)
Biol.Unit 1 (270 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
Authors
:
B. L. Hanson, J. M. Harp, D. E. Timm, G. J. Bunick
Date
:
06 Apr 00 (Deposition) - 17 Apr 00 (Release) - 13 Jul 11 (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
:
Nucleosome, Nucleosome Core Particle, Histone, Microgravity Histone Octamer, Dna Palindrome, Dna Protein Complex, Chromatin, Chromosomal Protein, Histone Fold, Bent Dna, Structural Protein-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. M. Harp, B. L. Hanson, D. E. Timm, G. J. Bunick
Asymmetries In The Nucleosome Core Particle At 2. 5 A Resolution.
Acta Crystallogr. , Sect. D V. 56 1513 2000
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
3e: POTASSIUM ION (Ke)
3f: POTASSIUM ION (Kf)
3g: POTASSIUM ION (Kg)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
4e: MANGANESE (II) ION (MNe)
4f: MANGANESE (II) ION (MNf)
4g: MANGANESE (II) ION (MNg)
4h: MANGANESE (II) ION (MNh)
4i: MANGANESE (II) ION (MNi)
4j: MANGANESE (II) ION (MNj)
4k: MANGANESE (II) ION (MNk)
4l: MANGANESE (II) ION (MNl)
4m: MANGANESE (II) ION (MNm)
4n: MANGANESE (II) ION (MNn)
4o: MANGANESE (II) ION (MNo)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
1
Ligand/Ion
CACODYLATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
K
-1
Ligand/Ion
POTASSIUM ION
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
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]
Sites
(25, 25)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:44 , GLY A:46 , ALA A:47 , THR B:90 , SER B:91
BINDING SITE FOR RESIDUE CL A 449
02
AC2
SOFTWARE
GLY E:44 , GLY E:46 , ALA E:47 , THR F:90 , SER F:91
BINDING SITE FOR RESIDUE CL E 450
03
AC3
SOFTWARE
GLU A:64 , GLN B:47 , VAL B:48 , HIS B:49 , GLU G:73 , GLN G:76 , ASP G:77 , LEU H:22
BINDING SITE FOR RESIDUE CAC G 451
04
AC4
SOFTWARE
DA J:255 , DA J:256
BINDING SITE FOR RESIDUE K J 452
05
AC5
SOFTWARE
LYS A:124 , DG J:216
BINDING SITE FOR RESIDUE K J 453
06
AC6
SOFTWARE
DG J:217
BINDING SITE FOR RESIDUE K J 454
07
AC7
SOFTWARE
DG J:227
BINDING SITE FOR RESIDUE K J 455
08
AC8
SOFTWARE
DA J:228
BINDING SITE FOR RESIDUE K J 456
09
AC9
SOFTWARE
DA J:175
BINDING SITE FOR RESIDUE K J 457
10
BC1
SOFTWARE
DG I:97 , DG I:98
BINDING SITE FOR RESIDUE K I 458
11
BC2
SOFTWARE
DG J:280 , HOH J:500 , HOH J:507
BINDING SITE FOR RESIDUE MN J 459
12
BC3
SOFTWARE
DG I:134 , HOH I:505
BINDING SITE FOR RESIDUE MN I 460
13
BC4
SOFTWARE
HOH I:509
BINDING SITE FOR RESIDUE MN J 461
14
BC5
SOFTWARE
DT I:140 , HOH I:511 , DG J:246
BINDING SITE FOR RESIDUE MN J 462
15
BC6
SOFTWARE
DG I:121 , HOH I:513
BINDING SITE FOR RESIDUE MN I 463
16
BC7
SOFTWARE
DG I:70 , DG I:71
BINDING SITE FOR RESIDUE MN I 464
17
BC8
SOFTWARE
DG I:39 , DG I:40 , HOH I:514
BINDING SITE FOR RESIDUE MN I 465
18
BC9
SOFTWARE
DG I:137 , DG I:138 , HOH I:488
BINDING SITE FOR RESIDUE MN I 466
19
CC1
SOFTWARE
DG J:185 , DG J:186
BINDING SITE FOR RESIDUE MN J 467
20
CC2
SOFTWARE
DG J:267 , HOH J:503
BINDING SITE FOR RESIDUE MN J 468
21
CC3
SOFTWARE
DA J:147
BINDING SITE FOR RESIDUE MN J 469
22
CC4
SOFTWARE
DG I:100
BINDING SITE FOR RESIDUE MN I 470
23
CC5
SOFTWARE
DA I:1
BINDING SITE FOR RESIDUE MN I 471
24
CC6
SOFTWARE
DA I:17 , DG I:18
BINDING SITE FOR RESIDUE MN I 472
25
CC7
SOFTWARE
DA I:124 , DG I:125
BINDING SITE FOR RESIDUE MN I 473
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 12)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H4 (D:14-18,H:14-18)
2: HISTONE_H2A (A:21-27,E:21-27)
3: HISTONE_H3_2 (C:66-74,G:66-74)
4: HISTONE_H2B (B:92-114,F:92-114)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H4
PS00047
Histone H4 signature.
H4_CHICK
15-19
2
D:14-18
H:14-18
2
HISTONE_H2A
PS00046
Histone H2A signature.
H2A4_CHICK
22-28
2
A:21-27
E:21-27
3
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H32_CHICK
67-75
2
C:66-74
G:66-74
4
HISTONE_H2B
PS00357
Histone H2B signature.
H2B1_CHICK
93-115
2
B:92-114
F:92-114
H2B7_CHICK
93-115
2
B:92-114
F:92-114
H2B5_CHICK
93-115
2
B:92-114
F:92-114
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1eqza_ (A:)
1b: SCOP_d1eqze_ (E:)
2a: SCOP_d1eqzb_ (B:)
2b: SCOP_d1eqzf_ (F:)
3a: SCOP_d1eqzc_ (C:)
3b: SCOP_d1eqzg_ (G:)
4a: SCOP_d1eqzd_ (D:)
4b: SCOP_d1eqzh_ (H:)
View:
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Classes
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)
(
)
Folds
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(
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Superfamilies
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)
(
)
Families
(
)
(
)
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)
Chicken (Gallus gallus), erythrocytes [TaxId: 9031]
(6)
1a
d1eqza_
A:
1b
d1eqze_
E:
Protein domain
:
Histone H2B
(48)
Chicken (Gallus gallus), erythrocytes [TaxId: 9031]
(6)
2a
d1eqzb_
B:
2b
d1eqzf_
F:
Protein domain
:
Histone H3
(58)
Chicken (Gallus gallus), erythrocytes [TaxId: 9031]
(6)
3a
d1eqzc_
C:
3b
d1eqzg_
G:
Protein domain
:
Histone H4
(60)
Chicken (Gallus gallus), erythrocytes [TaxId: 9031]
(6)
4a
d1eqzd_
D:
4b
d1eqzh_
H:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1eqzC00 (C:29-135)
1b: CATH_1eqzF00 (F:19-125)
1c: CATH_1eqzB00 (B:18-125)
1d: CATH_1eqzA00 (A:1-125)
1e: CATH_1eqzE00 (E:2-128)
1f: CATH_1eqzH00 (H:8-102)
1g: CATH_1eqzD00 (D:14-102)
1h: CATH_1eqzG00 (G:16-135)
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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)
[unclassified]
(10)
1a
1eqzC00
C:29-135
1b
1eqzF00
F:19-125
1c
1eqzB00
B:18-125
1d
1eqzA00
A:1-125
1e
1eqzE00
E:2-128
1f
1eqzH00
H:8-102
1g
1eqzD00
D:14-102
1h
1eqzG00
G:16-135
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Sidechain
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Ligand
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All Atoms
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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