PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3A6N
Asym. Unit
Info
Asym.Unit (248 KB)
Biol.Unit 1 (242 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE NUCLEOSOME CONTAINING A TESTIS-SPECIFIC HISTONE VARIANT, HUMAN H3T
Authors
:
H. Tachiwana, W. Kagawa, A. Osakabe, K. Koichiro, T. Shiga, H. Kimura, H. Kurumizaka
Date
:
04 Sep 09 (Deposition) - 26 May 10 (Release) - 18 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
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
[
close entry info
]
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
[
close Hetero Component info
]
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
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 2001
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 , DC J:225
BINDING SITE FOR RESIDUE MN I 201
07
AC7
SOFTWARE
DG I:121
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 1001
10
BC1
SOFTWARE
DG J:267
BINDING SITE FOR RESIDUE MN J 1002
11
BC2
SOFTWARE
DG J:217
BINDING SITE FOR RESIDUE MN J 1003
12
BC3
SOFTWARE
DG J:280
BINDING SITE FOR RESIDUE MN J 1004
[
close Site info
]
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)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:21-27,G:21-27)
2: HISTONE_H2B (D:92-114,H:92-114)
;
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_H2B
PS00357
Histone H2B signature.
H2B1J_HUMAN
93-115
2
D:92-114
H:92-114
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.1 (A:38-134 | E:38-135)
Exon 2.1 (B:22-102 | F:19-102)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
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
ENST00000366696
1
ENSE00001442338
chr1:
228613026-228612546
481
H31T_HUMAN
1-136
136
2
A:38-134
E:38-135
97
98
2.1
ENST00000377803
1
ENSE00001475159
chr6:
26104104-26104518
415
H4_HUMAN
1-127
127
2
B:22-102
F:19-102
81
84
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3a6nb_ (B:)
1b: SCOP_d3a6nc_ (C:)
1c: SCOP_d3a6nd_ (D:)
1d: SCOP_d3a6nf_ (F:)
1e: SCOP_d3a6ng_ (G:)
1f: SCOP_d3a6nh_ (H:)
2a: SCOP_d3a6na_ (A:)
2b: SCOP_d3a6ne_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d3a6nb_
B:
1b
d3a6nc_
C:
1c
d3a6nd_
D:
1d
d3a6nf_
F:
1e
d3a6ng_
G:
1f
d3a6nh_
H:
Protein domain
:
Histone H3
(58)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d3a6na_
A:
2b
d3a6ne_
E:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3a6nA00 (A:38-134)
1b: CATH_3a6nG00 (G:15-118)
1c: CATH_3a6nC00 (C:14-118)
1d: CATH_3a6nB00 (B:22-102)
1e: CATH_3a6nE00 (E:38-135)
1f: CATH_3a6nD00 (D:28-121)
1g: CATH_3a6nH00 (H:29-121)
1h: CATH_3a6nF00 (F:19-102)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
3a6nA00
A:38-134
1b
3a6nG00
G:15-118
1c
3a6nC00
C:14-118
1d
3a6nB00
B:22-102
1e
3a6nE00
E:38-135
1f
3a6nD00
D:28-121
1g
3a6nH00
H:29-121
1h
3a6nF00
F:19-102
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
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
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (248 KB)
Header - Asym.Unit
Biol.Unit 1 (242 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3A6N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
