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4DCK
Biol. Unit 1
Info
Asym.Unit (82 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (222 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE C-TERMINUS OF VOLTAGE-GATED SODIUM CHANNEL IN COMPLEX WITH FGF13 AND CAM
Authors
:
B. C. Chung, C. Wang, H. Yan, G. S. Pitt, S. Y. Lee
Date
:
17 Jan 12 (Deposition) - 27 Jun 12 (Release) - 25 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (3x)
Keywords
:
Iq-Motif, Ef-Hand, Voltage-Gated Sodium Channel Regulation, Nav1. 5 Ctd Binds To Fgf13 And Cam. Cam Binds To Ca2+. , Transport Protein- Transport Protein Regulator-Signaling Protein Complex, Transport Protein-Signaling Protein Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. Wang, B. C. Chung, H. Yan, S. Y. Lee, G. S. Pitt
Crystal Structure Of The Ternary Complex Of A Nav C-Termina Domain, A Fibroblast Growth Factor Homologous Factor, And Calmodulin.
Structure V. 20 1167 2012
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
View:
Select:
Label:
Sorry, no Info available
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:130 , ASP B:132 , ASP B:134 , GLN B:136 , HOH B:304 , HOH B:309
BINDING SITE FOR RESIDUE MG B 201
2
AC2
SOFTWARE
ASP B:81 , ASP B:132 , HOH B:301 , HOH B:303 , HOH B:311 , HOH B:358
BINDING SITE FOR RESIDUE MG B 202
3
AC3
SOFTWARE
ASP B:94 , ASP B:96 , ASN B:98 , TYR B:100 , HOH B:306 , HOH B:339
BINDING SITE FOR RESIDUE MG B 203
[
close Site info
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SAPs(SNPs)/Variants
(30, 30)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_069222 (N54I, chain B, )
02: VAR_048585 (M73T, chain B, )
03: VAR_073275 (F90L, chain B, )
04: VAR_073276 (D96V, chain B, )
05: VAR_073277 (N98I, chain B, )
06: VAR_069223 (N98S, chain B, )
07: VAR_073278 (D130G, chain B, )
08: VAR_073279 (D132E, chain B, )
09: VAR_073280 (D134H, chain B, )
10: VAR_073281 (Q136P, chain B, )
11: VAR_073282 (F142L, chain B, )
12: VAR_020945 (K144Q, chain C, )
13: VAR_055212 (V1777M, chain A, )
14: VAR_068339 (T1779M, chain A, )
15: VAR_008959 (E1784K, chain A, )
16: VAR_009938 (S1787N, chain A, )
17: VAR_001580 (D1790G, chain A, )
18: VAR_068475 (D1792N, chain A, )
19: VAR_019123 (Y1795C, chain A, )
20: VAR_019124 (Y1795H, chain A, )
21: VAR_036668 (D1819N, chain A, )
22: VAR_055213 (L1825P, chain A, )
23: VAR_055214 (R1826C, chain A, )
24: VAR_017687 (R1826H, chain A, )
25: VAR_001581 (D1839G, chain A, )
26: VAR_055215 (C1850S, chain A, )
27: VAR_055216 (M1875T, chain A, )
28: VAR_055217 (S1904L, chain A, )
29: VAR_068340 (Q1909R, chain A, )
30: VAR_017688 (A1924T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_069222
N
54
I
CALM_HUMAN
Disease (CPVT4)
---
B
N
54
I
02
UniProt
VAR_048585
M
73
T
CALM_HUMAN
Polymorphism
41389749
B
M
73
T
03
UniProt
VAR_073275
F
90
L
CALM_HUMAN
Disease (LQT14)
---
B
F
90
L
04
UniProt
VAR_073276
D
96
V
CALM_HUMAN
Disease (LQT15)
---
B
D
96
V
05
UniProt
VAR_073277
N
98
I
CALM_HUMAN
Disease (LQT15)
---
B
N
98
I
06
UniProt
VAR_069223
N
98
S
CALM_HUMAN
Disease (CPVT4)
---
B
N
98
S
07
UniProt
VAR_073278
D
130
G
CALM_HUMAN
Disease (LQT14)
---
B
D
130
G
08
UniProt
VAR_073279
D
132
E
CALM_HUMAN
Disease (LQT15)
---
B
D
132
E
09
UniProt
VAR_073280
D
134
H
CALM_HUMAN
Disease (LQT15)
---
B
D
134
H
10
UniProt
VAR_073281
Q
136
P
CALM_HUMAN
Disease (LQT15)
---
B
Q
136
P
11
UniProt
VAR_073282
F
142
L
CALM_HUMAN
Disease (LQT14)
---
B
F
142
L
12
UniProt
VAR_020945
K
197
Q
FGF13_HUMAN
Polymorphism
17510270
C
K
144
Q
13
UniProt
VAR_055212
V
1777
M
SCN5A_HUMAN
Disease (LQT3)
---
A
V
1777
M
14
UniProt
VAR_068339
T
1779
M
SCN5A_HUMAN
Disease (LQT3)
---
A
T
1779
M
15
UniProt
VAR_008959
E
1784
K
SCN5A_HUMAN
Disease (LQT3)
---
A
E
1784
K
16
UniProt
VAR_009938
S
1787
N
SCN5A_HUMAN
Disease (LQT3)
---
A
S
1787
N
17
UniProt
VAR_001580
D
1790
G
SCN5A_HUMAN
Disease (LQT3)
---
A
D
1790
G
18
UniProt
VAR_068475
D
1792
N
SCN5A_HUMAN
Disease (SSS1)
---
A
D
1792
N
19
UniProt
VAR_019123
Y
1795
C
SCN5A_HUMAN
Disease (LQT3)
---
A
Y
1795
C
20
UniProt
VAR_019124
Y
1795
H
SCN5A_HUMAN
Disease (BRGDA1)
---
A
Y
1795
H
21
UniProt
VAR_036668
D
1819
N
SCN5A_HUMAN
Disease (LQT3)
---
A
D
1819
N
22
UniProt
VAR_055213
L
1825
P
SCN5A_HUMAN
Disease (LQT3)
---
A
L
1825
P
23
UniProt
VAR_055214
R
1826
C
SCN5A_HUMAN
Disease (ATFB10)
---
A
R
1826
C
24
UniProt
VAR_017687
R
1826
H
SCN5A_HUMAN
Disease (LQT3)
---
A
R
1826
H
25
UniProt
VAR_001581
D
1839
G
SCN5A_HUMAN
Disease (LQT3)
---
A
D
1839
G
26
UniProt
VAR_055215
C
1850
S
SCN5A_HUMAN
Disease (BRGDA1)
---
A
C
1850
S
27
UniProt
VAR_055216
M
1875
T
SCN5A_HUMAN
Unclassified
---
A
M
1875
T
28
UniProt
VAR_055217
S
1904
L
SCN5A_HUMAN
Disease (LQT3)
---
A
S
1904
L
29
UniProt
VAR_068340
Q
1909
R
SCN5A_HUMAN
Disease (LQT3)
---
A
Q
1909
R
30
UniProt
VAR_017688
A
1924
T
SCN5A_HUMAN
Disease (BRGDA1)
---
A
A
1924
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 25)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 ()
2: EF_HAND_1 ()
3: HBGF_FGF (C:76-99)
;
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.
CALM1_HUMAN
8-43
44-79
81-116
117-149
4
B:8-43
B:44-79
B:81-116
B:117-149
CALM2_HUMAN
8-43
44-79
81-116
117-149
4
B:8-43
B:44-79
B:81-116
B:117-149
CALM3_HUMAN
8-43
44-79
81-116
117-149
4
B:8-43
B:44-79
B:81-116
B:117-149
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CALM1_HUMAN
21-33
57-69
94-106
130-142
4
B:21-33
B:62-69
B:94-106
B:130-142
CALM2_HUMAN
21-33
57-69
94-106
130-142
4
B:21-33
B:62-69
B:94-106
B:130-142
CALM3_HUMAN
21-33
57-69
94-106
130-142
4
B:21-33
B:62-69
B:94-106
B:130-142
3
HBGF_FGF
PS00247
HBGF/FGF family signature.
FGF13_HUMAN
129-152
1
C:76-99
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4dckb_ (B:)
2a: SCOP_d4dckc_ (C:)
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Classes
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Protein Domains
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Organisms
(
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(
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Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Calmodulin
(152)
Human (Homo sapiens) [TaxId: 9606]
(74)
1a
d4dckb_
B:
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Cytokine
(169)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d4dckc_
C:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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(currently selected atoms:
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)
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
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