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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
4CAK
Biol. Unit 1
Info
Asym.Unit (307 KB)
Biol.Unit 1 (299 KB)
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(1)
Title
:
THREE-DIMENSIONAL RECONSTRUCTION OF INTACT HUMAN INTEGRIN ALPHAIIBBETA3 IN A PHOSPHOLIPID BILAYER NANODISC
Authors
:
W. S. Choi, W. J. Rice, D. L. Stokes, B. S. Coller
Date
:
08 Oct 13 (Deposition) - 30 Oct 13 (Release) - 08 Jan 14 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
20.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cell Adhesion, Integrin, Single Particle Reconstruction
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. S. Choi, W. J. Rice, D. L. Stokes, B. S. Coller
Three-Dimensional Reconstruction Of Intact Human Integrin Alphaiibbeta3; New Implications For Activation-Dependent Ligand Binding.
Blood V. 122 4165 2013
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:2 , LEU A:3 , ASP A:4 , SER A:404 , PRO A:452 , ASN A:570 , VAL A:571 , SER A:572
BINDING SITE FOR RESIDUE NAG A3570
2
AC2
SOFTWARE
LEU A:264 , GLY A:282 , GLU A:283 , GLN A:284 , MET A:285 , ALA A:286 , LYS B:253 , ASN B:316 , LEU B:317 , GLN B:319 , ASN B:320 , SER B:510 , NAG B:3321
BINDING SITE FOR RESIDUE NAG B3320
3
AC3
SOFTWARE
ASN A:15
BINDING SITE FOR MONO-SACCHARIDE NAG A3015 BOUND TO ASN A 15
4
AC4
SOFTWARE
ASN B:99 , NAG B:3371
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B3099 THROUGH NAG B3100 BOUND TO ASN B 99
5
AC5
SOFTWARE
LEU A:600 , ASP A:601 , SER B:369 , ASN B:371 , SER B:398 , GLU B:400 , NAG B:3099
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B3371 THROUGH BMA B3373 BOUND TO ASN B 371
6
AC6
SOFTWARE
PRO A:564 , VAL A:566 , GLN A:595 , CYS A:608 , VAL A:609 , PRO A:610 , GLN A:611 , GLN A:613 , ALA A:638 , ASN A:639 , GLU A:640 , GLY A:641 , GLU A:642 , GLY A:643 , LYS A:694 , LYS A:695 , ASN A:696 , ALA A:697 , GLN A:698 , MET B:387 , ASN B:449 , ASN B:450 , GLY B:451 , ASN B:452
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B3452 THROUGH NAG B3453 BOUND TO ASN B 452
7
AC7
SOFTWARE
VAL B:529 , THR B:554 , TYR B:556 , TYR B:557 , ASN B:559 , ASP B:627 , GLU B:628 , ASN B:629 , THR B:630 , ARG B:633
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B3559 THROUGH MAN B3563 BOUND TO ASN B 559
8
AC8
SOFTWARE
GLU A:229 , SER A:261 , LEU A:264 , ARG A:281 , NAG B:3320
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B3321 THROUGH MAN B3323
[
close Site info
]
SAPs(SNPs)/Variants
(72, 72)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_014176 (T9I, chain A, )
02: VAR_003993 (L33P, chain B, )
03: VAR_069920 (C38Y, chain B, )
04: VAR_049633 (L40R, chain B, )
05: VAR_030445 (L55P, chain A, )
06: VAR_030473 (R93W, chain B, )
07: VAR_030446 (A108V, chain A, )
08: VAR_030474 (Y115C, chain B, )
09: VAR_010649 (L117W, chain B, )
10: VAR_069921 (M118R, chain B, )
11: VAR_030475 (D119N, chain B, )
12: VAR_003998 (D119Y, chain B, )
13: VAR_030476 (M124V, chain B, )
14: VAR_030447 (C130W, chain A, )
15: VAR_030477 (T140I, chain B, )
16: VAR_030448 (Y143H, chain A, )
17: VAR_003994 (R143Q, chain B, )
18: VAR_009885 (P145A, chain A, )
19: VAR_009886 (P145L, chain A, )
20: VAR_010651 (S162L, chain B, )
21: VAR_030449 (F171C, chain A, )
22: VAR_030450 (T176I, chain A, )
23: VAR_030451 (L183P, chain A, )
24: VAR_030452 (F191L, chain A, )
25: VAR_030478 (L196P, chain B, )
26: VAR_003999 (R214Q, chain B, )
27: VAR_004000 (R214W, chain B, )
28: VAR_030479 (R216Q, chain B, )
29: VAR_030480 (D217V, chain B, )
30: VAR_069922 (G221D, chain B, )
31: VAR_030453 (G236E, chain A, )
32: VAR_003979 (G242D, chain A, )
33: VAR_069923 (K253M, chain B, )
34: VAR_030481 (L262P, chain B, )
35: VAR_004001 (H280P, chain B, )
36: VAR_054820 (G282A, chain A, )
37: VAR_009887 (F289S, chain A, )
38: VAR_030482 (M295L, chain B, )
39: VAR_030454 (V298F, chain A, )
40: VAR_030483 (I304N, chain B, )
41: VAR_009888 (E324K, chain A, )
42: VAR_003980 (R327H, chain A, )
43: VAR_030455 (G349D, chain A, )
44: VAR_030456 (I374T, chain A, )
45: VAR_004002 (C374Y, chain B, )
46: VAR_030457 (G381R, chain A, )
47: VAR_003995 (P407A, chain B, )
48: VAR_003981 (G418D, chain A, )
49: VAR_014178 (V427I, chain B, )
50: VAR_003996 (R489Q, chain B, )
51: VAR_030484 (C506Y, chain B, )
52: VAR_010671 (C542R, chain B, )
53: VAR_030459 (A550D, chain A, )
54: VAR_004003 (C560F, chain B, )
55: VAR_030485 (C560R, chain B, )
56: VAR_030460 (I565T, chain A, )
57: VAR_004004 (G572S, chain B, )
58: VAR_030486 (C575R, chain B, )
59: VAR_010672 (G579S, chain B, )
60: VAR_054821 (V618L, chain A, )
61: VAR_003997 (R636C, chain B, )
62: VAR_030461 (C674R, chain A, )
63: VAR_030462 (L721V, chain A, )
64: VAR_030463 (R724P, chain A, )
65: VAR_003982 (Q747P, chain A, )
66: VAR_030464 (L816P, chain A, )
67: VAR_069917 (V903F, chain A, )
68: VAR_030465 (P912L, chain A, )
69: VAR_069918 (S926L, chain A, )
70: VAR_014177 (Y937N, chain A, )
71: VAR_030466 (V951M, chain A, )
72: VAR_030467 (A958T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014176
T
40
I
ITA2B_HUMAN
Polymorphism
5915
A
T
9
I
02
UniProt
VAR_003993
L
59
P
ITB3_HUMAN
Polymorphism
5918
B
L
33
P
03
UniProt
VAR_069920
C
64
Y
ITB3_HUMAN
Disease (GT)
---
B
C
38
Y
04
UniProt
VAR_049633
L
66
R
ITB3_HUMAN
Polymorphism
36080296
B
L
40
R
05
UniProt
VAR_030445
L
86
P
ITA2B_HUMAN
Disease (GT)
---
A
L
55
P
06
UniProt
VAR_030473
R
119
W
ITB3_HUMAN
Disease (GT)
---
B
R
93
W
07
UniProt
VAR_030446
A
139
V
ITA2B_HUMAN
Disease (GT)
---
A
A
108
V
08
UniProt
VAR_030474
Y
141
C
ITB3_HUMAN
Disease (GT)
---
B
Y
115
C
09
UniProt
VAR_010649
L
143
W
ITB3_HUMAN
Disease (GT)
---
B
L
117
W
10
UniProt
VAR_069921
M
144
R
ITB3_HUMAN
Disease (GT)
---
B
M
118
R
11
UniProt
VAR_030475
D
145
N
ITB3_HUMAN
Disease (GT)
---
B
D
119
N
12
UniProt
VAR_003998
D
145
Y
ITB3_HUMAN
Disease (GT)
---
B
D
119
Y
13
UniProt
VAR_030476
M
150
V
ITB3_HUMAN
Disease (GT)
---
B
M
124
V
14
UniProt
VAR_030447
C
161
W
ITA2B_HUMAN
Disease (GT)
---
A
C
130
W
15
UniProt
VAR_030477
T
166
I
ITB3_HUMAN
Unclassified
---
B
T
140
I
16
UniProt
VAR_030448
Y
174
H
ITA2B_HUMAN
Disease (GT)
---
A
Y
143
H
17
UniProt
VAR_003994
R
169
Q
ITB3_HUMAN
Polymorphism
5917
B
R
143
Q
18
UniProt
VAR_009885
P
176
A
ITA2B_HUMAN
Disease (GT)
---
A
P
145
A
19
UniProt
VAR_009886
P
176
L
ITA2B_HUMAN
Disease (GT)
---
A
P
145
L
20
UniProt
VAR_010651
S
188
L
ITB3_HUMAN
Disease (GT)
---
B
S
162
L
21
UniProt
VAR_030449
F
202
C
ITA2B_HUMAN
Disease (GT)
---
A
F
171
C
22
UniProt
VAR_030450
T
207
I
ITA2B_HUMAN
Disease (GT)
---
A
T
176
I
23
UniProt
VAR_030451
L
214
P
ITA2B_HUMAN
Disease (GT)
---
A
L
183
P
24
UniProt
VAR_030452
F
222
L
ITA2B_HUMAN
Disease (GT)
---
A
F
191
L
25
UniProt
VAR_030478
L
222
P
ITB3_HUMAN
Disease (GT)
---
B
L
196
P
26
UniProt
VAR_003999
R
240
Q
ITB3_HUMAN
Disease (GT)
---
B
R
214
Q
27
UniProt
VAR_004000
R
240
W
ITB3_HUMAN
Disease (GT)
---
B
R
214
W
28
UniProt
VAR_030479
R
242
Q
ITB3_HUMAN
Disease (GT)
---
B
R
216
Q
29
UniProt
VAR_030480
D
243
V
ITB3_HUMAN
Disease (GT)
---
B
D
217
V
30
UniProt
VAR_069922
G
247
D
ITB3_HUMAN
Disease (GT)
---
B
G
221
D
31
UniProt
VAR_030453
G
267
E
ITA2B_HUMAN
Disease (GT)
---
A
G
236
E
32
UniProt
VAR_003979
G
273
D
ITA2B_HUMAN
Disease (GT)
---
A
G
242
D
33
UniProt
VAR_069923
K
279
M
ITB3_HUMAN
Disease (GT)
---
B
K
253
M
34
UniProt
VAR_030481
L
288
P
ITB3_HUMAN
Disease (GT)
---
B
L
262
P
35
UniProt
VAR_004001
H
306
P
ITB3_HUMAN
Disease (GT)
13306476
B
H
280
P
36
UniProt
VAR_054820
G
313
A
ITA2B_HUMAN
Polymorphism
1126554
A
G
282
A
37
UniProt
VAR_009887
F
320
S
ITA2B_HUMAN
Disease (GT)
---
A
F
289
S
38
UniProt
VAR_030482
M
321
L
ITB3_HUMAN
Disease (GT)
---
B
M
295
L
39
UniProt
VAR_030454
V
329
F
ITA2B_HUMAN
Disease (GT)
---
A
V
298
F
40
UniProt
VAR_030483
I
330
N
ITB3_HUMAN
Disease (GT)
---
B
I
304
N
41
UniProt
VAR_009888
E
355
K
ITA2B_HUMAN
Disease (GT)
---
A
E
324
K
42
UniProt
VAR_003980
R
358
H
ITA2B_HUMAN
Disease (GT)
---
A
R
327
H
43
UniProt
VAR_030455
G
380
D
ITA2B_HUMAN
Disease (GT)
---
A
G
349
D
44
UniProt
VAR_030456
I
405
T
ITA2B_HUMAN
Disease (GT)
---
A
I
374
T
45
UniProt
VAR_004002
C
400
Y
ITB3_HUMAN
Disease (GT)
---
B
C
374
Y
46
UniProt
VAR_030457
G
412
R
ITA2B_HUMAN
Disease (GT)
---
A
G
381
R
47
UniProt
VAR_003995
P
433
A
ITB3_HUMAN
Polymorphism
121918448
B
P
407
A
48
UniProt
VAR_003981
G
449
D
ITA2B_HUMAN
Disease (GT)
---
A
G
418
D
49
UniProt
VAR_014178
V
453
I
ITB3_HUMAN
Polymorphism
5921
B
V
427
I
50
UniProt
VAR_003996
R
515
Q
ITB3_HUMAN
Polymorphism
13306487
B
R
489
Q
51
UniProt
VAR_030484
C
532
Y
ITB3_HUMAN
Disease (GT)
---
B
C
506
Y
52
UniProt
VAR_010671
C
568
R
ITB3_HUMAN
Disease (GT)
---
B
C
542
R
53
UniProt
VAR_030459
A
581
D
ITA2B_HUMAN
Disease (GT)
---
A
A
550
D
54
UniProt
VAR_004003
C
586
F
ITB3_HUMAN
Disease (GT)
---
B
C
560
F
55
UniProt
VAR_030485
C
586
R
ITB3_HUMAN
Disease (GT)
---
B
C
560
R
56
UniProt
VAR_030460
I
596
T
ITA2B_HUMAN
Disease (GT)
---
A
I
565
T
57
UniProt
VAR_004004
G
598
S
ITB3_HUMAN
Disease (GT)
---
B
G
572
S
58
UniProt
VAR_030486
C
601
R
ITB3_HUMAN
Disease (GT)
---
B
C
575
R
59
UniProt
VAR_010672
G
605
S
ITB3_HUMAN
Disease (GT)
---
B
G
579
S
60
UniProt
VAR_054821
V
649
L
ITA2B_HUMAN
Polymorphism
7207402
A
V
618
L
61
UniProt
VAR_003997
R
662
C
ITB3_HUMAN
Polymorphism
151219882
B
R
636
C
62
UniProt
VAR_030461
C
705
R
ITA2B_HUMAN
Disease (GT)
---
A
C
674
R
63
UniProt
VAR_030462
L
752
V
ITA2B_HUMAN
Disease (GT)
---
A
L
721
V
64
UniProt
VAR_030463
R
755
P
ITA2B_HUMAN
Disease (GT)
---
A
R
724
P
65
UniProt
VAR_003982
Q
778
P
ITA2B_HUMAN
Disease (GT)
---
A
Q
747
P
66
UniProt
VAR_030464
L
847
P
ITA2B_HUMAN
Disease (GT)
---
A
L
816
P
67
UniProt
VAR_069917
V
934
F
ITA2B_HUMAN
Disease (GT)
---
A
V
903
F
68
UniProt
VAR_030465
P
943
L
ITA2B_HUMAN
Disease (GT)
---
A
P
912
L
69
UniProt
VAR_069918
S
957
L
ITA2B_HUMAN
Disease (GT)
---
A
S
926
L
70
UniProt
VAR_014177
Y
968
N
ITA2B_HUMAN
Polymorphism
5914
A
Y
937
N
71
UniProt
VAR_030466
V
982
M
ITA2B_HUMAN
Disease (GT)
---
A
V
951
M
72
UniProt
VAR_030467
A
989
T
ITA2B_HUMAN
Polymorphism
78165611
A
A
958
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 13)
Info
All PROSITE Patterns/Profiles
1: FG_GAP (A:404-465)
2: EGF_1 ()
3: EGF_2 (B:460-473)
4: INTEGRIN_BETA ()
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FG_GAP
PS51470
FG-GAP repeat profile.
ITA2B_HUMAN
35-96
110-173
187-238
306-371
251-305
373-432
435-496
7
A:4-65
A:79-142
A:156-207
A:275-340
A:220-274
A:342-401
A:404-465
2
EGF_1
PS00022
EGF-like domain signature 1.
ITB3_HUMAN
486-497
573-584
2
B:460-471
B:547-558
3
EGF_2
PS01186
EGF-like domain signature 2.
ITB3_HUMAN
486-499
1
B:460-473
4
INTEGRIN_BETA
PS00243
Integrins beta chain cysteine-rich domain signature.
ITB3_HUMAN
521-534
562-575
601-614
3
B:495-508
B:536-549
B:575-588
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (307 KB)
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Biol.Unit 1 (299 KB)
Header - Biol.Unit 1
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