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1YDI
Asym. Unit
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Asym.Unit (59 KB)
Biol.Unit 1 (56 KB)
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(1)
Title
:
HUMAN VINCULIN HEAD DOMAIN (VH1, 1-258) IN COMPLEX WITH HUMAN ALPHA-ACTININ'S VINCULIN-BINDING SITE (RESIDUES 731-760)
Authors
:
T. Izard
Date
:
23 Dec 04 (Deposition) - 19 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cell Adhesion, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. R. Bois, R. A. Borgon, C. Vonrhein, T. Izard
Structural Dynamics Of {Alpha}-Actinin-Vinculin Interactions.
Mol. Cell. Biol. V. 14 6112 2005
(for further references see the
PDB file header
)
[
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]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
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]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037667 (V234L, chain A, )
2: VAR_072117 (N755D, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_037667
V
234
L
VINC_HUMAN
Polymorphism
17853882
A
V
234
L
2
UniProt
VAR_072117
N
748
D
ACTN4_HUMAN
Disease (FSGS1)
---
B
N
755
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: VINCULIN_1 (A:162-182)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VINCULIN_1
PS00663
Vinculin family talin-binding region signature.
VINC_HUMAN
162-182
1
A:162-182
[
close PROSITE info
]
Exons
(7, 7)
Info
All Exons
Exon 1.1a (A:1-56 (gaps))
Exon 1.2a (A:57-80)
Exon 1.4 (A:80-130)
Exon 1.5 (A:131-167)
Exon 1.6 (A:167-208)
Exon 1.7a (A:208-258)
Exon 2.20 (B:741-764)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7a
7: Boundary 1.7a/1.8
8: Boundary 2.19b/2.20
9: Boundary 2.20/2.21b
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
1.1a
ENST00000211998
1a
ENSE00002146319
chr10:
75757872-75758133
262
VINC_HUMAN
1-56
56
1
A:1-56 (gaps)
56
1.2a
ENST00000211998
2a
ENSE00001607712
chr10:
75802841-75802911
71
VINC_HUMAN
57-80
24
1
A:57-80
24
1.4
ENST00000211998
4
ENSE00001024254
chr10:
75830428-75830578
151
VINC_HUMAN
80-130
51
1
A:80-130
51
1.5
ENST00000211998
5
ENSE00001024245
chr10:
75830733-75830841
109
VINC_HUMAN
131-167
37
1
A:131-167
37
1.6
ENST00000211998
6
ENSE00001024249
chr10:
75832488-75832610
123
VINC_HUMAN
167-208
42
1
A:167-208
42
1.7a
ENST00000211998
7a
ENSE00001024263
chr10:
75834501-75834661
161
VINC_HUMAN
208-261
54
1
A:208-258
51
1.8
ENST00000211998
8
ENSE00001024248
chr10:
75842212-75842302
91
VINC_HUMAN
262-292
31
0
-
-
1.9a
ENST00000211998
9a
ENSE00000986356
chr10:
75843124-75843271
148
VINC_HUMAN
292-341
50
0
-
-
1.10
ENST00000211998
10
ENSE00000986357
chr10:
75848954-75849107
154
VINC_HUMAN
341-392
52
0
-
-
1.11
ENST00000211998
11
ENSE00000986358
chr10:
75849781-75849956
176
VINC_HUMAN
393-451
59
0
-
-
1.12
ENST00000211998
12
ENSE00001024262
chr10:
75854029-75854219
191
VINC_HUMAN
451-515
65
0
-
-
1.13
ENST00000211998
13
ENSE00000986360
chr10:
75855414-75855613
200
VINC_HUMAN
515-581
67
0
-
-
1.14
ENST00000211998
14
ENSE00000986361
chr10:
75856962-75857090
129
VINC_HUMAN
582-624
43
0
-
-
1.15a
ENST00000211998
15a
ENSE00000986362
chr10:
75860706-75860855
150
VINC_HUMAN
625-674
50
0
-
-
1.16
ENST00000211998
16
ENSE00000986363
chr10:
75863578-75863686
109
VINC_HUMAN
675-711
37
0
-
-
1.17c
ENST00000211998
17c
ENSE00000986364
chr10:
75864809-75865111
303
VINC_HUMAN
711-812
102
0
-
-
1.18
ENST00000211998
18
ENSE00000986365
chr10:
75866988-75867112
125
VINC_HUMAN
812-853
42
0
-
-
1.19b
ENST00000211998
19b
ENSE00000834577
chr10:
75868729-75868914
186
VINC_HUMAN
854-915
62
0
-
-
1.20
ENST00000211998
20
ENSE00000709651
chr10:
75871667-75871870
204
VINC_HUMAN
916-983
68
0
-
-
1.21
ENST00000211998
21
ENSE00000709670
chr10:
75873942-75874145
204
VINC_HUMAN
984-1051
68
0
-
-
1.22
ENST00000211998
22
ENSE00000986366
chr10:
75874553-75874657
105
VINC_HUMAN
1052-1086
35
0
-
-
1.23a
ENST00000211998
23a
ENSE00001373600
chr10:
75877781-75879910
2130
VINC_HUMAN
1087-1134
48
0
-
-
2.1a
ENST00000252699
1a
ENSE00001909908
chr19:
39138310-39138547
238
ACTN4_HUMAN
1-54
54
0
-
-
2.3b
ENST00000252699
3b
ENSE00001756201
chr19:
39191240-39191354
115
ACTN4_HUMAN
55-93
39
0
-
-
2.4
ENST00000252699
4
ENSE00001633778
chr19:
39191642-39191761
120
ACTN4_HUMAN
93-133
41
0
-
-
2.5
ENST00000252699
5
ENSE00001741382
chr19:
39195574-39195660
87
ACTN4_HUMAN
133-162
30
0
-
-
2.6
ENST00000252699
6
ENSE00001803629
chr19:
39196684-39196771
88
ACTN4_HUMAN
162-191
30
0
-
-
2.7
ENST00000252699
7
ENSE00001686766
chr19:
39198757-39198835
79
ACTN4_HUMAN
191-217
27
0
-
-
2.8b
ENST00000252699
8b
ENSE00001611972
chr19:
39200035-39200116
82
ACTN4_HUMAN
218-245
28
0
-
-
2.9
ENST00000252699
9
ENSE00000895787
chr19:
39200897-39200982
86
ACTN4_HUMAN
245-273
29
0
-
-
2.11
ENST00000252699
11
ENSE00000895786
chr19:
39205109-39205201
93
ACTN4_HUMAN
274-304
31
0
-
-
2.12c
ENST00000252699
12c
ENSE00001680426
chr19:
39207726-39207956
231
ACTN4_HUMAN
305-381
77
0
-
-
2.13
ENST00000252699
13
ENSE00001603394
chr19:
39208567-39208714
148
ACTN4_HUMAN
382-431
50
0
-
-
2.14a
ENST00000252699
14a
ENSE00000895781
chr19:
39212178-39212328
151
ACTN4_HUMAN
431-481
51
0
-
-
2.15b
ENST00000252699
15b
ENSE00000895780
chr19:
39214254-39214362
109
ACTN4_HUMAN
481-517
37
0
-
-
2.16
ENST00000252699
16
ENSE00000895779
chr19:
39214577-39214717
141
ACTN4_HUMAN
518-564
47
0
-
-
2.17
ENST00000252699
17
ENSE00000895778
chr19:
39214797-39214979
183
ACTN4_HUMAN
565-625
61
0
-
-
2.18a
ENST00000252699
18a
ENSE00000895777
chr19:
39215071-39215205
135
ACTN4_HUMAN
626-670
45
0
-
-
2.19b
ENST00000252699
19b
ENSE00001749718
chr19:
39216364-39216543
180
ACTN4_HUMAN
671-730
60
0
-
-
2.20
ENST00000252699
20
ENSE00001675072
chr19:
39217597-39217743
147
ACTN4_HUMAN
731-779
49
1
B:741-764
24
2.21b
ENST00000252699
21b
ENSE00000895774
chr19:
39218586-39218666
81
ACTN4_HUMAN
780-806
27
0
-
-
2.23
ENST00000252699
23
ENSE00000895773
chr19:
39219636-39219794
159
ACTN4_HUMAN
807-859
53
0
-
-
2.24d
ENST00000252699
24d
ENSE00001731568
chr19:
39219914-39222223
2310
ACTN4_HUMAN
860-911
52
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1ydia1 (A:-4-128)
1b: SCOP_d1ydia2 (A:129-258)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
alpha-catenin/vinculin-like
(25)
Family
:
alpha-catenin/vinculin
(24)
Protein domain
:
automated matches
(8)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1ydia1
A:-4-128
1b
d1ydia2
A:129-258
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ydiA02 (A:130-258)
2a: CATH_1ydiA01 (A:-4-129)
View:
Select:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.230, no name defined]
(23)
Human (Homo sapiens)
(11)
1a
1ydiA02
A:130-258
Topology
:
vbs2 fragment of talin
(15)
Homologous Superfamily
:
vbs2 fragment of talin
(15)
Human (Homo sapiens)
(7)
2a
1ydiA01
A:-4-129
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Spectrin_1ydiB01 (B:741-759)
2a: PFAM_Vinculin_1ydiA01 (A:3-258)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Spectrin]
(10)
Family
:
Spectrin
(10)
Homo sapiens (Human)
(8)
1a
Spectrin-1ydiB01
B:741-759
Clan
:
no clan defined [family: Vinculin]
(16)
Family
:
Vinculin
(16)
Homo sapiens (Human)
(8)
2a
Vinculin-1ydiA01
A:3-258
[
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]
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