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3CJC
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (123 KB)
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(1)
Title
:
ACTIN DIMER CROSS-LINKED BY V. CHOLERAE MARTX TOXIN AND COMPLEXED WITH DNASE I AND GELSOLIN-SEGMENT 1
Authors
:
M. R. Sawaya, D. S. Kudryashov, I. Pashkov, E. Reisler, T. O. Yeates
Date
:
12 Mar 08 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.90
Chains
:
Asym. Unit : A,D,G
Biol. Unit 1: A,D,G (1x)
Keywords
:
Cross-Linked Dimer, Atp-Binding, Cytoskeleton, Methylation, Muscle Protein, Nucleotide-Binding, Phosphoprotein, Structural Protein, Actin-Binding, Apoptosis, Endonuclease, Glycoprotein, Hydrolase, Nuclease, Nucleus, Secreted, Actin Capping, Alternative Initiation, Amyloid, Disease Mutation, Structural Protein-Hydrolase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. S. Kudryashov, Z. A. Durer, A. J. Ytterberg, M. R. Sawaya, I. Pashkov K. Prochazkova, T. O. Yeates, R. R. Loo, J. A. Loo, K. J. Satchell, E. Reisler
Connecting Actin Monomers By Iso-Peptide Bond Is A Toxicity Mechanism Of The Vibrio Cholerae Martx Toxin.
Proc. Natl. Acad. Sci. Usa V. 105 18537 2008
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
2
Ligand/Ion
CALCIUM ION
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN D:18 , THR D:20 , ALA D:248
BINDING SITE FOR RESIDUE NAG D 270
02
AC2
SOFTWARE
GLU D:244
BINDING SITE FOR RESIDUE NAG D 271
03
AC3
SOFTWARE
ASP A:11 , GLN A:137
BINDING SITE FOR RESIDUE CA A 401
04
AC4
SOFTWARE
ASN D:161 , ASP D:162 , GLY D:218 , SER D:219 , LEU D:220
BINDING SITE FOR RESIDUE SO4 D 272
05
AC5
SOFTWARE
ARG D:30 , THR D:62 , ARG D:85
BINDING SITE FOR RESIDUE SO4 D 273
06
AC6
SOFTWARE
ARG D:27 , ARG D:31 , TYR D:239
BINDING SITE FOR RESIDUE SO4 D 274
07
AC7
SOFTWARE
ARG A:147 , LYS A:328 , ILE A:330 , ARG G:96
BINDING SITE FOR RESIDUE SO4 G 126
08
AC8
SOFTWARE
GLY A:308 , ILE A:309 , ALA A:310 , ASP A:311
BINDING SITE FOR RESIDUE SO4 A 402
09
AC9
SOFTWARE
HIS D:64 , PHE D:84 , PRO D:86
BINDING SITE FOR RESIDUE SO4 D 275
10
BC1
SOFTWARE
GLY G:41 , ASP G:42 , GLU G:73 , HOH G:128 , HOH G:129
BINDING SITE FOR RESIDUE CA G 127
11
BC2
SOFTWARE
GLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:74 , ASP A:154 , GLY A:156 , ASP A:157 , GLY A:158 , GLY A:182 , LYS A:213 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306
BINDING SITE FOR RESIDUE ATP A 403
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024690 (A78T, chain G, )
2: VAR_DNAS1_BOVIN_001 (H121P, chain D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024690
A
129
T
GELS_HUMAN
Polymorphism
2230287
G
A
78
T
2
UniProt
VAR_DNAS1_BOVIN_001
*
H
143
P
DNAS1_BOVIN
---
---
D
H
121
P
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: ACTINS_1 (A:53-63)
2: ACTINS_ACT_LIKE (A:104-116)
3: DNASE_I_1 (D:130-150)
4: DNASE_I_2 (D:167-174)
5: ACTINS_2 (A:356-364)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACTINS_1
PS00406
Actins signature 1.
ACTS_RABIT
55-65
1
A:53-63
2
ACTINS_ACT_LIKE
PS01132
Actins and actin-related proteins signature.
ACTS_RABIT
106-118
1
A:104-116
3
DNASE_I_1
PS00919
Deoxyribonuclease I signature 1.
DNAS1_BOVIN
152-172
1
D:130-150
4
DNASE_I_2
PS00918
Deoxyribonuclease I signature 2.
DNAS1_BOVIN
189-196
1
D:167-174
5
ACTINS_2
PS00432
Actins signature 2.
ACTS_RABIT
358-366
1
A:356-364
[
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]
Exons
(11, 11)
Info
All Exons
Exon 1.2 (D:1-27)
Exon 1.3 (D:28-57)
Exon 1.4 (D:57-85)
Exon 1.5 (D:85-124 (gaps))
Exon 1.6 (D:124-161)
Exon 1.7 (D:162-213)
Exon 1.8 (D:213-245)
Exon 1.9 (D:246-260)
Exon 2.16d (G:1-66)
Exon 2.17 (G:66-117)
Exon 2.18b (G:118-125)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/-
10: Boundary 2.14/2.16d
11: Boundary 2.16d/2.17
12: Boundary 2.17/2.18b
13: Boundary 2.18b/2.18f
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
ENSBTAT00000026784
1
ENSBTAE00000293181
chr25:
3564711-3564829
119
DNAS1_BOVIN
-
0
0
-
-
1.2
ENSBTAT00000026784
2
ENSBTAE00000218065
chr25:
3565156-3565303
148
DNAS1_BOVIN
1-49
49
1
D:1-27
27
1.3
ENSBTAT00000026784
3
ENSBTAE00000420413
chr25:
3565639-3565727
89
DNAS1_BOVIN
50-79
30
1
D:28-57
30
1.4
ENSBTAT00000026784
4
ENSBTAE00000410212
chr25:
3565904-3565987
84
DNAS1_BOVIN
79-107
29
1
D:57-85
29
1.5
ENSBTAT00000026784
5
ENSBTAE00000218074
chr25:
3566232-3566347
116
DNAS1_BOVIN
107-146
40
1
D:85-124 (gaps)
40
1.6
ENSBTAT00000026784
6
ENSBTAE00000407443
chr25:
3566499-3566611
113
DNAS1_BOVIN
146-183
38
1
D:124-161
38
1.7
ENSBTAT00000026784
7
ENSBTAE00000398022
chr25:
3566701-3566855
155
DNAS1_BOVIN
184-235
52
1
D:162-213
52
1.8
ENSBTAT00000026784
8
ENSBTAE00000425804
chr25:
3567129-3567225
97
DNAS1_BOVIN
235-267
33
1
D:213-245
33
1.9
ENSBTAT00000026784
9
ENSBTAE00000293180
chr25:
3567369-3567733
365
DNAS1_BOVIN
268-282
15
1
D:246-260
15
2.14
ENST00000373818
14
ENSE00001461665
chr9:
124062071-124062283
213
GELS_HUMAN
1-48
48
0
-
-
2.16d
ENST00000373818
16d
ENSE00001725493
chr9:
124064241-124064445
205
GELS_HUMAN
49-117
69
1
G:1-66
66
2.17
ENST00000373818
17
ENSE00001745162
chr9:
124065189-124065343
155
GELS_HUMAN
117-168
52
1
G:66-117
52
2.18b
ENST00000373818
18b
ENSE00001764209
chr9:
124072962-124073123
162
GELS_HUMAN
169-222
54
1
G:118-125
8
2.18f
ENST00000373818
18f
ENSE00001689299
chr9:
124074617-124074766
150
GELS_HUMAN
223-272
50
0
-
-
2.18i
ENST00000373818
18i
ENSE00001727906
chr9:
124076212-124076301
90
GELS_HUMAN
273-302
30
0
-
-
2.19b
ENST00000373818
19b
ENSE00001732099
chr9:
124079364-124079496
133
GELS_HUMAN
303-347
45
0
-
-
2.20
ENST00000373818
20
ENSE00001734404
chr9:
124080684-124080772
89
GELS_HUMAN
347-376
30
0
-
-
2.21a
ENST00000373818
21a
ENSE00001618926
chr9:
124080943-124081158
216
GELS_HUMAN
377-448
72
0
-
-
2.22b
ENST00000373818
22b
ENSE00001591416
chr9:
124083546-124083679
134
GELS_HUMAN
449-493
45
0
-
-
2.23
ENST00000373818
23
ENSE00001735249
chr9:
124086832-124086922
91
GELS_HUMAN
493-523
31
0
-
-
2.24a
ENST00000373818
24a
ENSE00001704432
chr9:
124088790-124088960
171
GELS_HUMAN
524-580
57
0
-
-
2.25
ENST00000373818
25
ENSE00001668309
chr9:
124089586-124089760
175
GELS_HUMAN
581-639
59
0
-
-
2.26b
ENST00000373818
26b
ENSE00001721539
chr9:
124091169-124091293
125
GELS_HUMAN
639-680
42
0
-
-
2.26c
ENST00000373818
26c
ENSE00001771020
chr9:
124091516-124091593
78
GELS_HUMAN
681-706
26
0
-
-
2.27a
ENST00000373818
27a
ENSE00001779366
chr9:
124093666-124093726
61
GELS_HUMAN
707-727
21
0
-
-
2.28d
ENST00000373818
28d
ENSE00001732346
chr9:
124094712-124095120
409
GELS_HUMAN
727-782
56
0
-
-
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3cjcd1 (D:1-260)
2a: SCOP_d3cjcg1 (G:2-125)
View:
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Label:
Classes
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)
(
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Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNase I-like
(70)
Superfamily
:
DNase I-like
(70)
Family
:
DNase I-like
(31)
Protein domain
:
Deoxyribonuclease I
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
1a
d3cjcd1
D:1-260
Fold
:
Gelsolin-like
(96)
Superfamily
:
Actin depolymerizing proteins
(88)
Family
:
Gelsolin-like
(43)
Protein domain
:
Gelsolin
(33)
Human (Homo sapiens) [TaxId: 9606]
(31)
2a
d3cjcg1
G:2-125
[
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CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_3cjcA01 (A:6-34,A:71-134,A:337-372)
1b: CATH_3cjcA03 (A:136-181,A:271-332)
2a: CATH_3cjcG00 (G:1-125)
3a: CATH_3cjcD00 (D:1-260)
4a: CATH_3cjcA04 (A:182-267)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Rabbit (Oryctolagus cuniculus)
(44)
1a
3cjcA01
A:6-34,A:71-134,A:337-372
1b
3cjcA03
A:136-181,A:271-332
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Severin
(74)
Homologous Superfamily
:
Severin
(74)
Rabbit (Oryctolagus cuniculus)
(2)
2a
3cjcG00
G:1-125
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Deoxyribonuclease I; Chain A
(35)
Homologous Superfamily
:
[code=3.60.10.10, no name defined]
(35)
Rabbit (Oryctolagus cuniculus)
(7)
3a
3cjcD00
D:1-260
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Actin; Chain A, domain 4
(156)
Homologous Superfamily
:
Actin; Chain A, domain 4
(155)
Rabbit (Oryctolagus cuniculus)
(44)
4a
3cjcA04
A:182-267
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Chain G
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