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3AFA
Asym. Unit
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Asym.Unit (250 KB)
Biol.Unit 1 (245 KB)
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(1)
Title
:
THE HUMAN NUCLEOSOME STRUCTURE
Authors
:
H. Tachiwana, W. Kagawa, A. Osakabe, K. Koichiro, T. Shiga, H. Kimura, H. Kurumizaka
Date
:
24 Feb 10 (Deposition) - 26 May 10 (Release) - 18 Jul 12 (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
:
Histone-Fold, Dna-Binding Protein, Chromosomal Protein, Citrullination, Dna-Binding, Methylation, Nucleosome Core, Nucleus, Phosphoprotein, Isopeptide Bond, Antibiotic, Antimicrobial, Structural Protein-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Tachiwana, W. Kagawa, A. Osakabe, K. Kawaguchi, T. Shiga, Y. Hayashi-Takanaka, H. Kimura, H. Kurumizaka
Structural Basis Of Instability Of The Nucleosome Containin A Testis-Specific Histone Variant, Human H3T
Proc. Natl. Acad. Sci. Usa V. 107 10454 2010
[
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Hetero Components
(2, 12)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MN
8
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:120 , PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 201
02
AC2
SOFTWARE
GLY C:46 , ALA C:47 , THR D:90 , SER D:91
BINDING SITE FOR RESIDUE CL C 201
03
AC3
SOFTWARE
VAL D:48 , HOH D:301 , ASP E:77
BINDING SITE FOR RESIDUE MN D 201
04
AC4
SOFTWARE
LYS E:122
BINDING SITE FOR RESIDUE CL E 201
05
AC5
SOFTWARE
GLY G:44 , ALA G:45 , GLY G:46 , ALA G:47 , THR H:90 , SER H:91
BINDING SITE FOR RESIDUE CL G 201
06
AC6
SOFTWARE
DG I:68
BINDING SITE FOR RESIDUE MN I 201
07
AC7
SOFTWARE
DG I:121 , DG I:122 , DC J:171
BINDING SITE FOR RESIDUE MN I 202
08
AC8
SOFTWARE
DA I:133
BINDING SITE FOR RESIDUE MN I 203
09
AC9
SOFTWARE
DG J:185 , DG J:186
BINDING SITE FOR RESIDUE MN J 301
10
BC1
SOFTWARE
DG J:267
BINDING SITE FOR RESIDUE MN J 302
11
BC2
SOFTWARE
DG J:217
BINDING SITE FOR RESIDUE MN J 303
12
BC3
SOFTWARE
DG J:280
BINDING SITE FOR RESIDUE MN J 304
[
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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:
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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:92-114,H:92-114)
;
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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.
H2B1J_HUMAN
93-115
2
D:92-114
H:92-114
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Exons
(2, 4)
Info
All Exons
Exon 1.2b (A:38-134 | E:37-135)
Exon 2.1 (B:25-102 | F:19-102)
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All Exon Boundaries
1: Boundary -/1.2b
2: Boundary 1.2b/-
3: Boundary -/2.1
4: Boundary 2.1/-
View:
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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
1.2b
ENST00000359303
2b
ENSE00001974165
chr6:
27858570-27858160
411
H31_HUMAN
1-136
136
2
A:38-134
E:37-135
97
99
2.1
ENST00000377803
1
ENSE00001475159
chr6:
26104104-26104518
415
H4_HUMAN
1-127
127
2
B:25-102
F:19-102
78
84
[
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SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3afab_ (B:)
1b: SCOP_d3afac_ (C:)
1c: SCOP_d3afad_ (D:)
1d: SCOP_d3afaf_ (F:)
1e: SCOP_d3afag_ (G:)
1f: SCOP_d3afah_ (H:)
2a: SCOP_d3afaa_ (A:)
2b: SCOP_d3afae_ (E:)
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Classes
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Folds
(
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(
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(
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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
:
automated matches
(34)
Human (Homo sapiens) [TaxId: 9606]
(25)
1a
d3afab_
B:
1b
d3afac_
C:
1c
d3afad_
D:
1d
d3afaf_
F:
1e
d3afag_
G:
1f
d3afah_
H:
Protein domain
:
Histone H3
(58)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d3afaa_
A:
2b
d3afae_
E:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3afaA00 (A:38-134)
1b: CATH_3afaG00 (G:15-118)
1c: CATH_3afaC00 (C:11-118)
1d: CATH_3afaB00 (B:25-102)
1e: CATH_3afaE00 (E:37-135)
1f: CATH_3afaD00 (D:27-122)
1g: CATH_3afaH00 (H:30-121)
1h: CATH_3afaF00 (F:19-102)
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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
3afaA00
A:38-134
1b
3afaG00
G:15-118
1c
3afaC00
C:11-118
1d
3afaB00
B:25-102
1e
3afaE00
E:37-135
1f
3afaD00
D:27-122
1g
3afaH00
H:30-121
1h
3afaF00
F:19-102
[
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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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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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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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