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1J1D
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE 46KDA DOMAIN OF HUMAN CARDIAC TROPONIN IN THE CA2+ SATURATED FORM
Authors
:
S. Takeda, A. Yamashita, K. Maeda, Y. Maeda
Date
:
03 Dec 02 (Deposition) - 15 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.61
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Thin Filament, Muscle Regulation, Ca2+ Binding Protein, Ef- Hand, Coiled-Coil, Contractile Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Takeda, A. Yamashita, K. Maeda, Y. Maeda
Structure Of The Core Domain Of Human Cardiac Troponin In The Ca2+-Saturated Form
Nature V. 424 35 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:65 , ASP A:67 , SER A:69 , THR A:71 , ASP A:73 , GLU A:76
BINDING SITE FOR RESIDUE CA A 201
2
AC2
SOFTWARE
ASP A:105 , ASN A:107 , ASP A:109 , TYR A:111 , GLU A:116
BINDING SITE FOR RESIDUE CA A 202
3
AC3
SOFTWARE
ASP A:141 , ASN A:143 , ASP A:145 , ARG A:147 , ILE A:148 , GLU A:152
BINDING SITE FOR RESIDUE CA A 203
4
AC4
SOFTWARE
ASP D:65 , ASP D:67 , SER D:69 , THR D:71 , GLU D:76
BINDING SITE FOR RESIDUE CA D 201
5
AC5
SOFTWARE
ASP D:105 , ASN D:107 , ASP D:109 , TYR D:111 , ASP D:113 , GLU D:116
BINDING SITE FOR RESIDUE CA D 202
6
AC6
SOFTWARE
ASP D:141 , ASN D:143 , ASP D:145 , ARG D:147 , GLU D:152
BINDING SITE FOR RESIDUE CA D 203
[
close Site info
]
SAPs(SNPs)/Variants
(23, 41)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_063070 (A8V, chain A/D, )
02: VAR_019776 (L29Q, chain A/D, )
03: VAR_063548 (K36Q, chain C, )
04: VAR_029453 (R79C, chain C/F, )
05: VAR_016078 (P82S, chain C/F, )
06: VAR_063071 (S84Y, chain A/D, )
07: VAR_067264 (A116G, chain C/F, )
08: VAR_063072 (E134D, chain A/D, )
09: VAR_063073 (D145E, chain A/D, )
10: VAR_007603 (R145G, chain C, )
11: VAR_016080 (R145W, chain C, )
12: VAR_019873 (A157V, chain C/F, )
13: VAR_043988 (G159R, chain A/D, )
14: VAR_019874 (R162P, chain F, )
15: VAR_042745 (R162Q, chain F, )
16: VAR_043984 (R205L, chain B/E, )
17: VAR_042748 (I211T, chain B/E, )
18: VAR_057310 (I221T, chain B/E, )
19: VAR_013022 (T239T, chain B/E, )
20: VAR_007610 (E244D, chain B/E, )
21: VAR_007611 (K253R, chain B/E, )
22: VAR_029451 (N269Y, chain B/E, )
23: VAR_019879 (N271I, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_063070
A
8
V
TNNC1_HUMAN
Disease (CMH13)
---
A/D
A
8
V
02
UniProt
VAR_019776
L
29
Q
TNNC1_HUMAN
Disease (CMH13)
---
A/D
L
29
Q
03
UniProt
VAR_063548
K
36
Q
TNNI3_HUMAN
Disease (CMD1FF)
---
C
K
36
Q
04
UniProt
VAR_029453
R
79
C
TNNI3_HUMAN
Polymorphism
3729712
C/F
R
79
C
05
UniProt
VAR_016078
P
82
S
TNNI3_HUMAN
Disease (CMH7)
77615401
C/F
P
82
S
06
UniProt
VAR_063071
C
84
Y
TNNC1_HUMAN
Disease (CMH13)
---
A/D
S
84
Y
07
UniProt
VAR_067264
A
116
G
TNNI3_HUMAN
Disease (CMD1FF)
---
C/F
A
116
G
08
UniProt
VAR_063072
E
134
D
TNNC1_HUMAN
Disease (CMH13)
---
A/D
E
134
D
09
UniProt
VAR_063073
D
145
E
TNNC1_HUMAN
Disease (CMH13)
---
A/D
D
145
E
10
UniProt
VAR_007603
R
145
G
TNNI3_HUMAN
Disease (CMH7)
---
C
R
145
G
11
UniProt
VAR_016080
R
145
W
TNNI3_HUMAN
Disease (RCM1)
28934871
C
R
145
W
12
UniProt
VAR_019873
A
157
V
TNNI3_HUMAN
Disease (CMH7)
---
C/F
A
157
V
13
UniProt
VAR_043988
G
159
R
TNNC1_HUMAN
Disease (CMD1Z)
---
A/D
G
159
R
14
UniProt
VAR_019874
R
162
P
TNNI3_HUMAN
Disease (CMH7)
---
F
R
162
P
15
UniProt
VAR_042745
R
162
Q
TNNI3_HUMAN
Disease (CMH7)
---
F
R
162
Q
16
UniProt
VAR_043984
R
215
L
TNNT2_HUMAN
Disease (CMD1D)
---
B/E
R
205
L
17
UniProt
VAR_042748
I
221
T
TNNT2_HUMAN
Polymorphism
45520032
B/E
I
211
T
18
UniProt
VAR_057310
I
231
T
TNNT2_HUMAN
Polymorphism
45520032
B/E
I
221
T
19
UniProt
VAR_013022
S
249
T
TNNT2_HUMAN
Polymorphism
---
B/E
T
239
T
20
UniProt
VAR_007610
E
254
D
TNNT2_HUMAN
Disease (CMH2)
45466197
B/E
E
244
D
21
UniProt
VAR_007611
K
263
R
TNNT2_HUMAN
Polymorphism
---
B/E
K
253
R
22
UniProt
VAR_029451
N
279
Y
TNNT2_HUMAN
Polymorphism
4523540
B/E
N
269
Y
23
UniProt
VAR_019879
N
281
I
TNNT2_HUMAN
Disease (CMH2)
---
B/E
N
271
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 14)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (A:33-51,D:33-51|A:52-87,D:52-87|A:...)
2: EF_HAND_1 (A:65-77,D:65-77|A:105-117,D:105-11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
TNNC1_HUMAN
33-51
52-87
92-127
128-161
8
A:33-51
D:33-51
A:52-87
D:52-87
A:92-127
D:92-127
A:128-161
D:128-161
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
TNNC1_HUMAN
65-77
105-117
141-153
6
A:65-77
D:65-77
A:105-117
D:105-117
A:141-153
D:141-153
[
close PROSITE info
]
Exons
(15, 29)
Info
All Exons
Exon 1.1 (A:1-8 | D:2-8)
Exon 1.2b (A:9-19 | D:9-19)
Exon 1.3 (A:19-68 | D:19-68)
Exon 1.4b (A:68-106 (gaps) | D:68-106)
Exon 1.5c (A:106-152 | D:106-152)
Exon 1.6 (A:152-161 | D:152-161)
Exon 2.11b (B:202-225 | E:200-225)
Exon 2.12a (B:225-255 | E:225-255)
Exon 2.13 (B:256-269 | E:256-269)
Exon 2.14e (B:269-271 | E:269-274)
Exon 3.3 (C:35-36 | -)
Exon 3.4 (C:37-50 | F:37-50)
Exon 3.5 (C:51-94 | F:51-94)
Exon 3.6 (C:95-124 | F:95-124)
Exon 3.7 (C:125-160 (gaps) | F:125-162 (gaps...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2b
03: Boundary 1.2b/1.3
04: Boundary 1.3/1.4b
05: Boundary 1.4b/1.5c
06: Boundary 1.5c/1.6
07: Boundary 1.6/-
08: Boundary 2.10a/2.11b
09: Boundary 2.11b/2.12a
10: Boundary 2.12a/2.13
11: Boundary 2.13/2.14e
12: Boundary 2.14e/-
13: Boundary 3.2/3.3
14: Boundary 3.3/3.4
15: Boundary 3.4/3.5
16: Boundary 3.5/3.6
17: Boundary 3.6/3.7
18: Boundary 3.7/3.8
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
ENST00000232975
1
ENSE00001063786
chr3:
52488086-52488008
79
TNNC1_HUMAN
1-8
8
2
A:1-8
D:2-8
8
7
1.2b
ENST00000232975
2b
ENSE00000770833
chr3:
52486529-52486499
31
TNNC1_HUMAN
9-19
11
2
A:9-19
D:9-19
11
11
1.3
ENST00000232975
3
ENSE00000770832
chr3:
52486268-52486122
147
TNNC1_HUMAN
19-68
50
2
A:19-68
D:19-68
50
50
1.4b
ENST00000232975
4b
ENSE00000770831
chr3:
52485874-52485760
115
TNNC1_HUMAN
68-106
39
2
A:68-106 (gaps)
D:68-106
39
39
1.5c
ENST00000232975
5c
ENSE00000770830
chr3:
52485543-52485407
137
TNNC1_HUMAN
106-152
47
2
A:106-152
D:106-152
47
47
1.6
ENST00000232975
6
ENSE00001063787
chr3:
52485322-52485118
205
TNNC1_HUMAN
152-161
10
2
A:152-161
D:152-161
10
10
2.2g
ENST00000236918
2g
ENSE00001315772
chr1:
201342382-201342342
41
TNNT2_HUMAN
1-14
14
0
-
-
2.3a
ENST00000236918
3a
ENSE00001686085
chr1:
201341283-201341273
11
TNNT2_HUMAN
14-18
5
0
-
-
2.4a
ENST00000236918
4a
ENSE00001444197
chr1:
201338973-201338944
30
TNNT2_HUMAN
18-28
11
0
-
-
2.5b
ENST00000236918
5b
ENSE00001233153
chr1:
201337355-201337290
66
TNNT2_HUMAN
28-50
23
0
-
-
2.6b
ENST00000236918
6b
ENSE00001043765
chr1:
201336934-201336899
36
TNNT2_HUMAN
50-62
13
0
-
-
2.7c
ENST00000236918
7c
ENSE00000796482
chr1:
201335999-201335966
34
TNNT2_HUMAN
62-73
12
0
-
-
2.7f
ENST00000236918
7f
ENSE00000796481
chr1:
201334798-201334738
61
TNNT2_HUMAN
73-93
21
0
-
-
2.8c
ENST00000236918
8c
ENSE00000796480
chr1:
201334435-201334319
117
TNNT2_HUMAN
94-132
39
0
-
-
2.9a
ENST00000236918
9a
ENSE00001043748
chr1:
201333503-201333426
78
TNNT2_HUMAN
133-158
26
0
-
-
2.9g
ENST00000236918
9g
ENSE00001715169
chr1:
201332534-201332424
111
TNNT2_HUMAN
159-195
37
0
-
-
2.10a
ENST00000236918
10a
ENSE00001798058
chr1:
201331522-201331514
9
TNNT2_HUMAN
196-198
3
0
-
-
2.11b
ENST00000236918
11b
ENSE00001786343
chr1:
201331150-201331041
110
TNNT2_HUMAN
199-235
37
2
B:202-225
E:200-225
24
26
2.12a
ENST00000236918
12a
ENSE00001773452
chr1:
201330497-201330407
91
TNNT2_HUMAN
235-265
31
2
B:225-255
E:225-255
31
31
2.13
ENST00000236918
13
ENSE00001709786
chr1:
201328791-201328751
41
TNNT2_HUMAN
266-279
14
2
B:256-269
E:256-269
14
14
2.14e
ENST00000236918
14e
ENSE00001749651
chr1:
201328383-201328142
242
TNNT2_HUMAN
279-293
15
2
B:269-271
E:269-274
3
6
3.1
ENST00000344887
1
ENSE00001524342
chr19:
55669100-55668947
154
TNNI3_HUMAN
1-4
4
0
-
-
3.2
ENST00000344887
2
ENSE00001758167
chr19:
55668676-55668664
13
TNNI3_HUMAN
4-8
5
0
-
-
3.3
ENST00000344887
3
ENSE00001250420
chr19:
55668501-55668418
84
TNNI3_HUMAN
9-36
28
1
C:35-36
-
2
-
3.4
ENST00000344887
4
ENSE00000727912
chr19:
55668012-55667971
42
TNNI3_HUMAN
37-50
14
2
C:37-50
F:37-50
14
14
3.5
ENST00000344887
5
ENSE00000727909
chr19:
55667700-55667569
132
TNNI3_HUMAN
51-94
44
2
C:51-94
F:51-94
44
44
3.6
ENST00000344887
6
ENSE00000417663
chr19:
55666198-55666109
90
TNNI3_HUMAN
95-124
30
2
C:95-124
F:95-124
30
30
3.7
ENST00000344887
7
ENSE00000856455
chr19:
55665574-55665398
177
TNNI3_HUMAN
125-183
59
2
C:125-160 (gaps)
F:125-162 (gaps)
36
38
3.8
ENST00000344887
8
ENSE00001250409
chr19:
55663285-55663138
148
TNNI3_HUMAN
184-210
27
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1j1da_ (A:)
1b: SCOP_d1j1dd_ (D:)
2a: SCOP_d1j1dc_ (C:)
2b: SCOP_d1j1df_ (F:)
3a: SCOP_d1j1db_ (B:)
3b: SCOP_d1j1de_ (E:)
View:
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Folds
(
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Superfamilies
(
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Troponin C
(53)
Human (Homo sapiens), cardiac isoform [TaxId: 9606]
(16)
1a
d1j1da_
A:
1b
d1j1dd_
D:
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Troponin coil-coiled subunits
(8)
Family
:
Troponin I
(4)
Protein domain
:
Troponin I
(4)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1j1dc_
C:
2b
d1j1df_
F:
Family
:
Troponin T
(4)
Protein domain
:
Troponin T
(4)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d1j1db_
B:
3b
d1j1de_
E:
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1j1dA01 (A:13-87)
1b: CATH_1j1dD01 (D:5-93)
1c: CATH_1j1dD02 (D:94-157)
1d: CATH_1j1dA02 (A:88-152)
2a: CATH_1j1dF01 (F:37-138)
2b: CATH_1j1dC01 (C:35-146)
2c: CATH_1j1dE00 (E:200-274)
2d: CATH_1j1dB00 (B:202-271)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Human (Homo sapiens)
(106)
1a
1j1dA01
A:13-87
1b
1j1dD01
D:5-93
1c
1j1dD02
D:94-157
1d
1j1dA02
A:88-152
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.350, no name defined]
(3)
Human (Homo sapiens)
(2)
2a
1j1dF01
F:37-138
2b
1j1dC01
C:35-146
2c
1j1dE00
E:200-274
2d
1j1dB00
B:202-271
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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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
Asymmetric Unit 1
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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)
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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") .
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