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Asym. Unit
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Asym.Unit (340 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (167 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN FULL-LENGTH VINCULIN (RESIDUES 1-1066)
Authors
:
R. A. Borgon, C. Vonrhein, G. Bricogne, P. R. Bois, T. Izard
Date
:
19 Jun 04 (Deposition) - 15 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Actin-Binding, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Borgon, C. Vonrhein, G. Bricogne, P. R. Bois, T. Izard
Crystal Structure Of Human Vinculin
Structure V. 12 1189 2004
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(1, 72)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1ag: SELENOMETHIONINE (MSEag)
1ah: SELENOMETHIONINE (MSEah)
1ai: SELENOMETHIONINE (MSEai)
1aj: SELENOMETHIONINE (MSEaj)
1ak: SELENOMETHIONINE (MSEak)
1al: SELENOMETHIONINE (MSEal)
1am: SELENOMETHIONINE (MSEam)
1an: SELENOMETHIONINE (MSEan)
1ao: SELENOMETHIONINE (MSEao)
1ap: SELENOMETHIONINE (MSEap)
1aq: SELENOMETHIONINE (MSEaq)
1ar: SELENOMETHIONINE (MSEar)
1as: SELENOMETHIONINE (MSEas)
1at: SELENOMETHIONINE (MSEat)
1au: SELENOMETHIONINE (MSEau)
1av: SELENOMETHIONINE (MSEav)
1aw: SELENOMETHIONINE (MSEaw)
1ax: SELENOMETHIONINE (MSEax)
1ay: SELENOMETHIONINE (MSEay)
1az: SELENOMETHIONINE (MSEaz)
1b: SELENOMETHIONINE (MSEb)
1ba: SELENOMETHIONINE (MSEba)
1bb: SELENOMETHIONINE (MSEbb)
1bc: SELENOMETHIONINE (MSEbc)
1bd: SELENOMETHIONINE (MSEbd)
1be: SELENOMETHIONINE (MSEbe)
1bf: SELENOMETHIONINE (MSEbf)
1bg: SELENOMETHIONINE (MSEbg)
1bh: SELENOMETHIONINE (MSEbh)
1bi: SELENOMETHIONINE (MSEbi)
1bj: SELENOMETHIONINE (MSEbj)
1bk: SELENOMETHIONINE (MSEbk)
1bl: SELENOMETHIONINE (MSEbl)
1bm: SELENOMETHIONINE (MSEbm)
1bn: SELENOMETHIONINE (MSEbn)
1bo: SELENOMETHIONINE (MSEbo)
1bp: SELENOMETHIONINE (MSEbp)
1bq: SELENOMETHIONINE (MSEbq)
1br: SELENOMETHIONINE (MSEbr)
1bs: SELENOMETHIONINE (MSEbs)
1bt: SELENOMETHIONINE (MSEbt)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
72
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037667 (V234L, chain A/B, )
2: VAR_035101 (L277M, chain A/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/B
V
234
L
2
UniProt
VAR_035101
L
277
M
VINC_HUMAN
Disease (CMH15)
---
A/B
L
277
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: VINCULIN_1 (A:162-182,B:162-182)
2: VINCULIN_2 (A:277-287,B:277-287|A:388-398,B:38...)
;
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
2
A:162-182
B:162-182
2
VINCULIN_2
PS00664
Vinculin repeated domain signature.
VINC_HUMAN
277-287
388-398
497-507
6
A:277-287
B:277-287
A:388-398
B:388-398
A:497-507
B:497-507
[
close PROSITE info
]
Exons
(21, 42)
Info
All Exons
Exon 1.1a (A:1-56 | B:1-56)
Exon 1.2a (A:57-80 | B:57-80)
Exon 1.4 (A:80-130 | B:80-130)
Exon 1.5 (A:131-167 | B:131-167)
Exon 1.6 (A:167-208 | B:167-208)
Exon 1.7a (A:208-261 | B:208-261)
Exon 1.8 (A:262-292 | B:262-292)
Exon 1.9a (A:292-341 | B:292-341)
Exon 1.10 (A:341-392 | B:341-392)
Exon 1.11 (A:393-451 | B:393-451)
Exon 1.12 (A:451-515 | B:451-515)
Exon 1.13 (A:515-581 | B:515-581)
Exon 1.14 (A:582-624 | B:582-624)
Exon 1.15a (A:625-674 | B:625-674)
Exon 1.16 (A:675-711 | B:675-711)
Exon 1.17c (A:711-812 | B:711-812)
Exon 1.18 (A:812-843 | B:812-843)
Exon 1.19b (A:877-915 | B:877-915)
Exon 1.21 (A:916-983 | B:916-983)
Exon 1.22 (A:984-1018 | B:984-1018)
Exon 1.23a (A:1019-1061 | B:1019-1062)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2a
03: Boundary 1.2a/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7a
07: Boundary 1.7a/1.8
08: Boundary 1.8/1.9a
09: Boundary 1.9a/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15a
15: Boundary 1.15a/1.16
16: Boundary 1.16/1.17c
17: Boundary 1.17c/1.18
18: Boundary 1.18/1.19b
19: Boundary 1.19b/1.20
20: Boundary 1.20/1.21
21: Boundary 1.21/1.22
22: Boundary 1.22/1.23a
23: Boundary 1.23a/-
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
2
A:1-56
B:1-56
56
56
1.2a
ENST00000211998
2a
ENSE00001607712
chr10:
75802841-75802911
71
VINC_HUMAN
57-80
24
2
A:57-80
B:57-80
24
24
1.4
ENST00000211998
4
ENSE00001024254
chr10:
75830428-75830578
151
VINC_HUMAN
80-130
51
2
A:80-130
B:80-130
51
51
1.5
ENST00000211998
5
ENSE00001024245
chr10:
75830733-75830841
109
VINC_HUMAN
131-167
37
2
A:131-167
B:131-167
37
37
1.6
ENST00000211998
6
ENSE00001024249
chr10:
75832488-75832610
123
VINC_HUMAN
167-208
42
2
A:167-208
B:167-208
42
42
1.7a
ENST00000211998
7a
ENSE00001024263
chr10:
75834501-75834661
161
VINC_HUMAN
208-261
54
2
A:208-261
B:208-261
54
54
1.8
ENST00000211998
8
ENSE00001024248
chr10:
75842212-75842302
91
VINC_HUMAN
262-292
31
2
A:262-292
B:262-292
31
31
1.9a
ENST00000211998
9a
ENSE00000986356
chr10:
75843124-75843271
148
VINC_HUMAN
292-341
50
2
A:292-341
B:292-341
50
50
1.10
ENST00000211998
10
ENSE00000986357
chr10:
75848954-75849107
154
VINC_HUMAN
341-392
52
2
A:341-392
B:341-392
52
52
1.11
ENST00000211998
11
ENSE00000986358
chr10:
75849781-75849956
176
VINC_HUMAN
393-451
59
2
A:393-451
B:393-451
59
59
1.12
ENST00000211998
12
ENSE00001024262
chr10:
75854029-75854219
191
VINC_HUMAN
451-515
65
2
A:451-515
B:451-515
65
65
1.13
ENST00000211998
13
ENSE00000986360
chr10:
75855414-75855613
200
VINC_HUMAN
515-581
67
2
A:515-581
B:515-581
67
67
1.14
ENST00000211998
14
ENSE00000986361
chr10:
75856962-75857090
129
VINC_HUMAN
582-624
43
2
A:582-624
B:582-624
43
43
1.15a
ENST00000211998
15a
ENSE00000986362
chr10:
75860706-75860855
150
VINC_HUMAN
625-674
50
2
A:625-674
B:625-674
50
50
1.16
ENST00000211998
16
ENSE00000986363
chr10:
75863578-75863686
109
VINC_HUMAN
675-711
37
2
A:675-711
B:675-711
37
37
1.17c
ENST00000211998
17c
ENSE00000986364
chr10:
75864809-75865111
303
VINC_HUMAN
711-812
102
2
A:711-812
B:711-812
102
102
1.18
ENST00000211998
18
ENSE00000986365
chr10:
75866988-75867112
125
VINC_HUMAN
812-853
42
2
A:812-843
B:812-843
32
32
1.19b
ENST00000211998
19b
ENSE00000834577
chr10:
75868729-75868914
186
VINC_HUMAN
854-915
62
2
A:877-915
B:877-915
39
39
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
2
A:916-983
B:916-983
68
68
1.22
ENST00000211998
22
ENSE00000986366
chr10:
75874553-75874657
105
VINC_HUMAN
1052-1086
35
2
A:984-1018
B:984-1018
35
35
1.23a
ENST00000211998
23a
ENSE00001373600
chr10:
75877781-75879910
2130
VINC_HUMAN
1087-1134
48
2
A:1019-1061
B:1019-1062
43
44
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1tr2A05 (A:896-1061)
1b: CATH_1tr2B05 (B:896-1062)
1c: CATH_1tr2A04 (A:719-835)
1d: CATH_1tr2B04 (B:719-835)
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(
)
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)
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
1tr2A05
A:896-1061
1b
1tr2B05
B:896-1062
1c
1tr2A04
A:719-835
1d
1tr2B04
B:719-835
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Vinculin_1tr2B01 (B:916-1062)
1b: PFAM_Vinculin_1tr2B02 (B:916-1062)
1c: PFAM_Vinculin_1tr2B03 (B:916-1062)
1d: PFAM_Vinculin_1tr2B04 (B:916-1062)
1e: PFAM_Vinculin_1tr2B05 (B:916-1062)
1f: PFAM_Vinculin_1tr2B06 (B:916-1062)
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Clans
(
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Families
(
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(
)
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(
)
(
)
Clan
:
no clan defined [family: Vinculin]
(16)
Family
:
Vinculin
(16)
Homo sapiens (Human)
(8)
1a
Vinculin-1tr2B01
B:916-1062
1b
Vinculin-1tr2B02
B:916-1062
1c
Vinculin-1tr2B03
B:916-1062
1d
Vinculin-1tr2B04
B:916-1062
1e
Vinculin-1tr2B05
B:916-1062
1f
Vinculin-1tr2B06
B:916-1062
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