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1T44
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (176 KB)
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(1)
Title
:
STRUCTURAL BASIS OF ACTIN SEQUESTRATION BY THYMOSIN-B4: IMPLICATIONS FOR ARP2/3 ACTIVATION
Authors
:
E. Irobi, A. H. Aguda, M. Larsson, L. D. Burtnick, R. C. Robinson
Date
:
28 Apr 04 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,G
Biol. Unit 1: A,G (1x)
Keywords
:
Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Irobi, A. H. Aguda, M. Larsson, C. Guerin, H. L. Yin, L. D. Burtnick, L. Blanchoin, R. C. Robinson
Structural Basis Of Actin Sequestration By Thymosin-Beta4: Implications For Wh2 Proteins.
Embo J. V. 23 3599 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
3
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ATP A:900 , HOH A:909 , HOH A:911 , HOH A:915 , HOH A:918 , HOH A:970
BINDING SITE FOR RESIDUE CA A 700
2
AC2
SOFTWARE
GLU A:167 , ASP G:109 , GLY G:114 , ALA G:116 , HOH G:712 , HOH G:724 , HOH G:729
BINDING SITE FOR RESIDUE CA G 701
3
AC3
SOFTWARE
GLY G:65 , ASP G:66 , GLU G:97 , VAL G:145 , HOH G:704 , HOH G:730
BINDING SITE FOR RESIDUE CA G 702
4
AC4
SOFTWARE
GLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:156 , ASP A:157 , GLY A:158 , VAL A:159 , GLY A:182 , ARG A:210 , LYS A:213 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , CA A:700 , HOH A:904 , HOH A:911 , HOH A:915 , HOH A:949 , HOH A:992 , HOH A:999 , HOH A:1022
BINDING SITE FOR RESIDUE ATP A 900
[
close Site info
]
SAPs(SNPs)/Variants
(74, 74)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_011680 (G15R, chain A, )
02: VAR_062425 (D25N, chain A, )
03: VAR_062426 (V35L, chain A, )
04: VAR_062427 (P38L, chain A, )
05: VAR_062431 (I64N, chain A, )
06: VAR_062432 (T66I, chain A, )
07: VAR_062433 (E72K, chain A, )
08: VAR_062434 (H73L, chain A, )
09: VAR_062435 (H73R, chain A, )
10: VAR_062436 (I75L, chain A, )
11: VAR_062437 (T77A, chain A, )
12: VAR_062438 (E83K, chain A, )
13: VAR_011681 (L94P, chain A, )
14: VAR_024690 (A102T, chain G, )
15: VAR_062439 (A114T, chain A, )
16: VAR_011682 (N115S, chain A, )
17: VAR_062440 (N115T, chain A, )
18: VAR_062441 (R116H, chain A, )
19: VAR_013470 (M132V, chain A, )
20: VAR_062442 (V134A, chain A, )
21: VAR_011683 (I136M, chain A, )
22: VAR_062443 (A138P, chain A, )
23: VAR_062444 (L140P, chain A, )
24: VAR_062445 (G146D, chain A, )
25: VAR_062446 (T148N, chain A, )
26: VAR_062447 (D154N, chain A, )
27: VAR_011684 (V163L, chain A, )
28: VAR_062448 (V163M, chain A, )
29: VAR_062449 (A170G, chain A, )
30: VAR_062450 (D179G, chain A, )
31: VAR_062451 (D179H, chain A, )
32: VAR_062452 (D179N, chain A, )
33: VAR_015580 (G182D, chain A, )
34: VAR_015582 (R183C, chain A, )
35: VAR_062453 (R183D, chain A, )
36: VAR_015581 (R183G, chain A, )
37: VAR_062454 (R183S, chain A, )
38: VAR_062455 (R196L, chain A, )
39: VAR_062456 (G197S, chain A, )
40: VAR_032917 (L221P, chain A, )
41: VAR_062457 (E224G, chain A, )
42: VAR_062458 (E224Q, chain A, )
43: VAR_062459 (N225V, chain A, )
44: VAR_062460 (M227I, chain A, )
45: VAR_062461 (M227T, chain A, )
46: VAR_062462 (M227V, chain A, )
47: VAR_062463 (E241K, chain A, )
48: VAR_062464 (Q246K, chain A, )
49: VAR_062465 (Q246R, chain A, )
50: VAR_062466 (G251D, chain A, )
51: VAR_015583 (R256H, chain A, )
52: VAR_062467 (R256L, chain A, )
53: VAR_011685 (E259V, chain A, )
54: VAR_015584 (Q263L, chain A, )
55: VAR_011686 (G268C, chain A, )
56: VAR_062468 (G268D, chain A, )
57: VAR_062469 (G268R, chain A, )
58: VAR_013471 (M269R, chain A, )
59: VAR_062470 (A272E, chain A, )
60: VAR_062471 (Y279H, chain A, )
61: VAR_015585 (N280K, chain A, )
62: VAR_062472 (M283K, chain A, )
63: VAR_015586 (D286G, chain A, )
64: VAR_032918 (D292V, chain A, )
65: VAR_032919 (P332S, chain A, )
66: VAR_062473 (E334A, chain A, )
67: VAR_062474 (K336E, chain A, )
68: VAR_062475 (K336I, chain A, )
69: VAR_062476 (S348L, chain A, )
70: VAR_015587 (I357L, chain A, )
71: VAR_011687 (V370F, chain A, )
72: VAR_062477 (R372S, chain A, )
73: VAR_062478 (K373E, chain A, )
74: VAR_062479 (K373Q, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_011680
G
17
R
ACTS_HUMAN
Disease (MPCETM)
---
A
G
15
R
02
UniProt
VAR_062425
D
27
N
ACTS_HUMAN
Disease (NEM3)
---
A
D
25
N
03
UniProt
VAR_062426
V
37
L
ACTS_HUMAN
Disease (NEM3)
---
A
V
35
L
04
UniProt
VAR_062427
P
40
L
ACTS_HUMAN
Disease (NEM3)
---
A
P
38
L
05
UniProt
VAR_062431
I
66
N
ACTS_HUMAN
Disease (NEM3)
---
A
I
64
N
06
UniProt
VAR_062432
T
68
I
ACTS_HUMAN
Disease (NEM3)
---
A
T
66
I
07
UniProt
VAR_062433
E
74
K
ACTS_HUMAN
Disease (NEM3)
---
A
E
72
K
08
UniProt
VAR_062434
H
75
L
ACTS_HUMAN
Disease (NEM3)
---
A
H
73
L
09
UniProt
VAR_062435
H
75
R
ACTS_HUMAN
Disease (NEM3)
---
A
H
73
R
10
UniProt
VAR_062436
I
77
L
ACTS_HUMAN
Disease (NEM3)
---
A
I
75
L
11
UniProt
VAR_062437
T
79
A
ACTS_HUMAN
Disease (NEM3)
---
A
T
77
A
12
UniProt
VAR_062438
E
85
K
ACTS_HUMAN
Disease (NEM3)
---
A
E
83
K
13
UniProt
VAR_011681
L
96
P
ACTS_HUMAN
Disease (NEM3)
---
A
L
94
P
14
UniProt
VAR_024690
A
129
T
GELS_HUMAN
Polymorphism
2230287
G
A
102
T
15
UniProt
VAR_062439
A
116
T
ACTS_HUMAN
Disease (NEM3)
---
A
A
114
T
16
UniProt
VAR_011682
N
117
S
ACTS_HUMAN
Disease (NEM3)
---
A
N
115
S
17
UniProt
VAR_062440
N
117
T
ACTS_HUMAN
Disease (NEM3)
---
A
N
115
T
18
UniProt
VAR_062441
R
118
H
ACTS_HUMAN
Disease (NEM3)
---
A
R
116
H
19
UniProt
VAR_013470
M
134
V
ACTS_HUMAN
Disease (NEM3)
---
A
M
132
V
20
UniProt
VAR_062442
V
136
A
ACTS_HUMAN
Disease (NEM3)
---
A
V
134
A
21
UniProt
VAR_011683
I
138
M
ACTS_HUMAN
Disease (NEM3)
---
A
I
136
M
22
UniProt
VAR_062443
A
140
P
ACTS_HUMAN
Disease (NEM3)
---
A
A
138
P
23
UniProt
VAR_062444
L
142
P
ACTS_HUMAN
Disease (NEM3)
---
A
L
140
P
24
UniProt
VAR_062445
G
148
D
ACTS_HUMAN
Disease (NEM3)
---
A
G
146
D
25
UniProt
VAR_062446
T
150
N
ACTS_HUMAN
Disease (NEM3)
---
A
T
148
N
26
UniProt
VAR_062447
D
156
N
ACTS_HUMAN
Disease (NEM3)
---
A
D
154
N
27
UniProt
VAR_011684
V
165
L
ACTS_HUMAN
Disease (MPCETM)
---
A
V
163
L
28
UniProt
VAR_062448
V
165
M
ACTS_HUMAN
Disease (NEM3)
---
A
V
163
M
29
UniProt
VAR_062449
A
172
G
ACTS_HUMAN
Disease (NEM3)
---
A
A
170
G
30
UniProt
VAR_062450
D
181
G
ACTS_HUMAN
Disease (NEM3)
---
A
D
179
G
31
UniProt
VAR_062451
D
181
H
ACTS_HUMAN
Disease (NEM3)
---
A
D
179
H
32
UniProt
VAR_062452
D
181
N
ACTS_HUMAN
Disease (NEM3)
---
A
D
179
N
33
UniProt
VAR_015580
G
184
D
ACTS_HUMAN
Disease (NEM3)
---
A
G
182
D
34
UniProt
VAR_015582
R
185
C
ACTS_HUMAN
Disease (NEM3)
---
A
R
183
C
35
UniProt
VAR_062453
R
185
D
ACTS_HUMAN
Disease (NEM3)
---
A
R
183
D
36
UniProt
VAR_015581
R
185
G
ACTS_HUMAN
Disease (NEM3)
---
A
R
183
G
37
UniProt
VAR_062454
R
185
S
ACTS_HUMAN
Disease (NEM3)
---
A
R
183
S
38
UniProt
VAR_062455
R
198
L
ACTS_HUMAN
Disease (NEM3)
---
A
R
196
L
39
UniProt
VAR_062456
G
199
S
ACTS_HUMAN
Disease (NEM3)
---
A
G
197
S
40
UniProt
VAR_032917
L
223
P
ACTS_HUMAN
Disease (CFTD)
---
A
L
221
P
41
UniProt
VAR_062457
E
226
G
ACTS_HUMAN
Disease (NEM3)
---
A
E
224
G
42
UniProt
VAR_062458
E
226
Q
ACTS_HUMAN
Disease (NEM3)
---
A
E
224
Q
43
UniProt
VAR_062459
N
227
V
ACTS_HUMAN
Disease (NEM3)
---
A
N
225
V
44
UniProt
VAR_062460
M
229
I
ACTS_HUMAN
Disease (NEM3)
---
A
M
227
I
45
UniProt
VAR_062461
M
229
T
ACTS_HUMAN
Disease (NEM3)
---
A
M
227
T
46
UniProt
VAR_062462
M
229
V
ACTS_HUMAN
Disease (NEM3)
---
A
M
227
V
47
UniProt
VAR_062463
E
243
K
ACTS_HUMAN
Disease (NEM3)
---
A
E
241
K
48
UniProt
VAR_062464
Q
248
K
ACTS_HUMAN
Disease (NEM3)
---
A
Q
246
K
49
UniProt
VAR_062465
Q
248
R
ACTS_HUMAN
Disease (NEM3)
---
A
Q
246
R
50
UniProt
VAR_062466
G
253
D
ACTS_HUMAN
Disease (NEM3)
---
A
G
251
D
51
UniProt
VAR_015583
R
258
H
ACTS_HUMAN
Disease (NEM3)
---
A
R
256
H
52
UniProt
VAR_062467
R
258
L
ACTS_HUMAN
Disease (NEM3)
---
A
R
256
L
53
UniProt
VAR_011685
E
261
V
ACTS_HUMAN
Disease (NEM3)
---
A
E
259
V
54
UniProt
VAR_015584
Q
265
L
ACTS_HUMAN
Disease (NEM3)
---
A
Q
263
L
55
UniProt
VAR_011686
G
270
C
ACTS_HUMAN
Disease (NEM3)
---
A
G
268
C
56
UniProt
VAR_062468
G
270
D
ACTS_HUMAN
Disease (NEM3)
---
A
G
268
D
57
UniProt
VAR_062469
G
270
R
ACTS_HUMAN
Disease (NEM3)
---
A
G
268
R
58
UniProt
VAR_013471
M
271
R
ACTS_HUMAN
Disease (NEM3)
---
A
M
269
R
59
UniProt
VAR_062470
A
274
E
ACTS_HUMAN
Disease (NEM3)
---
A
A
272
E
60
UniProt
VAR_062471
Y
281
H
ACTS_HUMAN
Disease (NEM3)
---
A
Y
279
H
61
UniProt
VAR_015585
N
282
K
ACTS_HUMAN
Disease (NEM3)
---
A
N
280
K
62
UniProt
VAR_062472
M
285
K
ACTS_HUMAN
Disease (NEM3)
---
A
M
283
K
63
UniProt
VAR_015586
D
288
G
ACTS_HUMAN
Disease (NEM3)
---
A
D
286
G
64
UniProt
VAR_032918
D
294
V
ACTS_HUMAN
Disease (CFTD)
---
A
D
292
V
65
UniProt
VAR_032919
P
334
S
ACTS_HUMAN
Disease (CFTD)
---
A
P
332
S
66
UniProt
VAR_062473
E
336
A
ACTS_HUMAN
Disease (NEM3)
---
A
E
334
A
67
UniProt
VAR_062474
K
338
E
ACTS_HUMAN
Disease (NEM3)
---
A
K
336
E
68
UniProt
VAR_062475
K
338
I
ACTS_HUMAN
Disease (NEM3)
---
A
K
336
I
69
UniProt
VAR_062476
S
350
L
ACTS_HUMAN
Disease (NEM3)
---
A
S
348
L
70
UniProt
VAR_015587
I
359
L
ACTS_HUMAN
Disease (NEM3)
---
A
I
357
L
71
UniProt
VAR_011687
V
372
F
ACTS_HUMAN
Disease (NEM3)
---
A
V
370
F
72
UniProt
VAR_062477
R
374
S
ACTS_HUMAN
Disease (NEM3)
---
A
R
372
S
73
UniProt
VAR_062478
K
375
E
ACTS_HUMAN
Disease (NEM3)
---
A
K
373
E
74
UniProt
VAR_062479
K
375
Q
ACTS_HUMAN
Disease (NEM3)
---
A
K
373
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: THYMOSIN_B4 (G:141-160)
2: ACTINS_1 (A:53-63,A:53-63,A:53-63,A:53-63,A:...)
3: ACTINS_ACT_LIKE (A:104-116,A:104-116,A:104-116,A:10...)
4: ACTINS_2 (A:356-364,A:356-364,A:356-364,A:35...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYMOSIN_B4
PS00500
Thymosin beta-4 family signature.
TYB4_MOUSE
24-35
1
G:141-160
2
ACTINS_1
PS00406
Actins signature 1.
ACTS_BOVIN
55-65
1
A:53-63
ACTS_CHICK
55-65
1
A:53-63
ACTS_HUMAN
55-65
1
A:53-63
ACTS_MOUSE
55-65
1
A:53-63
ACTS_PIG
55-65
1
A:53-63
ACTS_RABIT
55-65
1
A:53-63
ACTS_RAT
55-65
1
A:53-63
3
ACTINS_ACT_LIKE
PS01132
Actins and actin-related proteins signature.
ACTS_BOVIN
106-118
1
A:104-116
ACTS_CHICK
106-118
1
A:104-116
ACTS_HUMAN
106-118
1
A:104-116
ACTS_MOUSE
106-118
1
A:104-116
ACTS_PIG
106-118
1
A:104-116
ACTS_RABIT
106-118
1
A:104-116
ACTS_RAT
106-118
1
A:104-116
4
ACTINS_2
PS00432
Actins signature 2.
ACTS_BOVIN
358-366
1
A:356-364
ACTS_CHICK
358-366
1
A:356-364
ACTS_HUMAN
358-366
1
A:356-364
ACTS_MOUSE
358-366
1
A:356-364
ACTS_PIG
358-366
1
A:356-364
ACTS_RABIT
358-366
1
A:356-364
ACTS_RAT
358-366
1
A:356-364
[
close PROSITE info
]
Exons
(6, 6)
Info
All Exons
Exon 1.2 (A:6-38)
Exon 1.3 (A:51-150)
Exon 1.4 (A:150-204)
Exon 1.5 (A:204-268)
Exon 1.6 (A:268-328)
Exon 1.7 (A:329-375)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/-
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
ENSRNOT00000024084
1
ENSRNOE00000354839
chr19:
54084508-54084458
51
ACTS_RAT
-
0
0
-
-
1.2
ENSRNOT00000024084
2
ENSRNOE00000251177
chr19:
54083476-54083336
141
ACTS_RAT
1-43
43
1
A:6-38
33
1.3
ENSRNOT00000024084
3
ENSRNOE00000328109
chr19:
54083239-54082915
325
ACTS_RAT
44-152
109
1
A:51-150
100
1.4
ENSRNOT00000024084
4
ENSRNOE00000279898
chr19:
54082725-54082564
162
ACTS_RAT
152-206
55
1
A:150-204
55
1.5
ENSRNOT00000024084
5
ENSRNOE00000321788
chr19:
54082465-54082274
192
ACTS_RAT
206-270
65
1
A:204-268
65
1.6
ENSRNOT00000024084
6
ENSRNOE00000319688
chr19:
54082138-54081957
182
ACTS_RAT
270-330
61
1
A:268-328
61
1.7
ENSRNOT00000024084
7
ENSRNOE00000251161
chr19:
54081880-54081498
383
ACTS_RAT
331-377
47
1
A:329-375
47
[
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SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1t44g_ (G:)
2a: SCOP_d1t44a1 (A:6-146)
2b: SCOP_d1t44a2 (A:147-375)
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(
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(
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(
)
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)
(
)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Gelsolin-like
(96)
Superfamily
:
Actin depolymerizing proteins
(88)
Family
:
Gelsolin-like
(43)
Protein domain
:
Gelsolin
(33)
Human (Homo sapiens) [TaxId: 9606]
(31)
1a
d1t44g_
G:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Actin/HSP70
(199)
Protein domain
:
Actin
(69)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(55)
2a
d1t44a1
A:6-146
2b
d1t44a2
A:147-375
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CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_1t44A01 (A:6-34,A:71-134,A:337-363)
1b: CATH_1t44A03 (A:136-181,A:271-332)
2a: CATH_1t44G00 (G:28-171)
3a: CATH_1t44A04 (A:182-267)
4a: CATH_1t44A02 (A:35-68)
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(
)
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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)
Human, house mouse (Homo sapiens, mus musculus)
(1)
1a
1t44A01
A:6-34,A:71-134,A:337-363
1b
1t44A03
A:136-181,A:271-332
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Severin
(74)
Homologous Superfamily
:
Severin
(74)
Human, house mouse (Homo sapiens, mus musculus)
(1)
2a
1t44G00
G:28-171
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Actin; Chain A, domain 4
(156)
Homologous Superfamily
:
Actin; Chain A, domain 4
(155)
Human, house mouse (Homo sapiens, mus musculus)
(1)
3a
1t44A04
A:182-267
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Actin; Chain A, domain 2
(36)
Homologous Superfamily
:
Actin; Chain A, domain 2
(36)
Human, house mouse (Homo sapiens, mus musculus)
(1)
4a
1t44A02
A:35-68
[
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Gelsolin_1t44G01 (G:48-131)
2a: PFAM_Actin_1t44A01 (A:6-375)
3a: PFAM_Thymosin_1t44G02 (G:153-171)
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Clans
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)
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)
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)
(
)
Organisms
(
)
(
)
Clan
:
ADF
(44)
Family
:
Gelsolin
(23)
Homo sapiens (Human)
(13)
1a
Gelsolin-1t44G01
G:48-131
Clan
:
Actin_ATPase
(173)
Family
:
Actin
(70)
Oryctolagus cuniculus (Rabbit)
(47)
2a
Actin-1t44A01
A:6-375
Clan
:
no clan defined [family: Thymosin]
(2)
Family
:
Thymosin
(2)
Mus musculus (Mouse)
(1)
3a
Thymosin-1t44G02
G:153-171
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