PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1U7V
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (99 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE PHOSPHORYLATED SMAD2/SMAD4 HETEROTRIMERIC COMPLEX
Authors
:
B. M. Chacko, B. Y. Qin, A. Tiwari, G. Shi, S. Lam, L. J. Hayward, M. De Caestecker, K. Lin
Date
:
04 Aug 04 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Smad, Tgf-Beta, Signal Transduction, Protein Complex, Phosphorylation, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. M. Chacko, B. Y. Qin, A. Tiwari, G. Shi, S. Lam, L. J. Hayward, M. De Caestecker, K. Lin
Structural Basis Of Heteromeric Smad Protein Assembly In Tgf-Beta Signaling
Mol. Cell V. 15 813 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: PHOSPHOSERINE (SEPa)
1b: PHOSPHOSERINE (SEPb)
1c: PHOSPHOSERINE (SEPc)
1d: PHOSPHOSERINE (SEPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SEP
4
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(16, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_036473 (D300V, chain A/C, )
02: VAR_022833 (E330G, chain B, )
03: VAR_036476 (D351N, chain B, )
04: VAR_SMAD4_HUMAN_CCDS11950_1_02 (D351N, chain B, )
05: VAR_019571 (G352R, chain B, )
06: VAR_019572 (R361C, chain B, )
07: VAR_036477 (R361H, chain B, )
08: VAR_SMAD4_HUMAN_CCDS11950_1_03 (R361H, chain B, )
09: VAR_019573 (G386D, chain B, )
10: VAR_011377 (L440R, chain A/C, )
11: VAR_011378 (P445H, chain A/C, )
12: VAR_011379 (D450E, chain A/C, )
13: VAR_011380 (D493H, chain B, )
14: VAR_067602 (I500M, chain B, )
15: VAR_067603 (I500T, chain B, )
16: VAR_067604 (I500V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_036473
D
300
V
SMAD2_HUMAN
Unclassified
---
A/C
D
300
V
02
UniProt
VAR_022833
E
330
G
SMAD4_HUMAN
Disease (JPS)
281875324
B
E
330
G
03
UniProt
VAR_036476
D
351
N
SMAD4_HUMAN
Unclassified
---
B
D
351
N
04
CancerSNP
VAR_SMAD4_HUMAN_CCDS11950_1_02
*
D
351
N
SMAD4_HUMAN
Disease (Colorectal cancer)
---
B
D
351
N
05
UniProt
VAR_019571
G
352
R
SMAD4_HUMAN
Disease (JPS)
121912581
B
G
352
R
06
UniProt
VAR_019572
R
361
C
SMAD4_HUMAN
Disease (JPS)
80338963
B
R
361
C
07
UniProt
VAR_036477
R
361
H
SMAD4_HUMAN
Unclassified
---
B
R
361
H
08
CancerSNP
VAR_SMAD4_HUMAN_CCDS11950_1_03
*
R
361
H
SMAD4_HUMAN
Disease (Colorectal cancer)
---
B
R
361
H
09
UniProt
VAR_019573
G
386
D
SMAD4_HUMAN
Disease (JP/HHT)
28936393
B
G
386
D
10
UniProt
VAR_011377
L
440
R
SMAD2_HUMAN
Unclassified
---
A/C
L
440
R
11
UniProt
VAR_011378
P
445
H
SMAD2_HUMAN
Unclassified
---
A/C
P
445
H
12
UniProt
VAR_011379
D
450
E
SMAD2_HUMAN
Unclassified
---
A/C
D
450
E
13
UniProt
VAR_011380
D
493
H
SMAD4_HUMAN
Unclassified
28936392
B
D
493
H
14
UniProt
VAR_067602
I
500
M
SMAD4_HUMAN
Disease (MYHRS)
281875320
B
I
500
M
15
UniProt
VAR_067603
I
500
T
SMAD4_HUMAN
Disease (MYHRS)
281875321
B
I
500
T
16
UniProt
VAR_067604
I
500
V
SMAD4_HUMAN
Disease (MYHRS)
281875322
B
I
500
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: MH2 (A:274-467,C:274-467,B:323-549)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MH2
PS51076
MAD homology domain 2 (MH2) profile.
SMAD2_HUMAN
274-467
2
A:274-467
C:274-467
SMAD4_HUMAN
323-552
1
B:323-549
[
close PROSITE info
]
Exons
(9, 13)
Info
All Exons
Exon 1.9 (A:270-333 | C:272-333)
Exon 1.10 (A:333-379 | C:333-379)
Exon 1.11 (A:379-427 | C:379-427)
Exon 1.12b (A:427-467 | C:427-467)
Exon 2.10 (B:314-319)
Exon 2.11 (B:319-380)
Exon 2.12 (B:380-436)
Exon 2.13 (B:437-461)
Exon 2.14b (B:490-549)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.8/1.9
02: Boundary 1.9/1.10
03: Boundary 1.10/1.11
04: Boundary 1.11/1.12b
05: Boundary 1.12b/-
06: Boundary 2.9/2.10
07: Boundary 2.10/2.11
08: Boundary 2.11/2.12
09: Boundary 2.12/2.13
10: Boundary 2.13/2.14b
11: Boundary 2.14b/-
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
1.2
ENST00000262160
2
ENSE00001533831
chr18:
45456930-45456732
199
SMAD2_HUMAN
-
0
0
-
-
1.3
ENST00000262160
3
ENSE00001191187
chr18:
45423180-45422892
289
SMAD2_HUMAN
1-79
79
0
-
-
1.4
ENST00000262160
4
ENSE00001248514
chr18:
45396935-45396846
90
SMAD2_HUMAN
79-109
31
0
-
-
1.5
ENST00000262160
5
ENSE00001248509
chr18:
45395807-45395614
194
SMAD2_HUMAN
109-174
66
0
-
-
1.6
ENST00000262160
6
ENSE00001248503
chr18:
45394828-45394694
135
SMAD2_HUMAN
174-219
46
0
-
-
1.7
ENST00000262160
7
ENSE00001728507
chr18:
45391504-45391430
75
SMAD2_HUMAN
219-244
26
0
-
-
1.8
ENST00000262160
8
ENSE00001248493
chr18:
45377698-45377645
54
SMAD2_HUMAN
244-262
19
0
-
-
1.9
ENST00000262160
9
ENSE00001248484
chr18:
45375058-45374846
213
SMAD2_HUMAN
262-333
72
2
A:270-333
C:272-333
64
62
1.10
ENST00000262160
10
ENSE00001248481
chr18:
45372171-45372034
138
SMAD2_HUMAN
333-379
47
2
A:333-379
C:333-379
47
47
1.11
ENST00000262160
11
ENSE00001598119
chr18:
45371855-45371711
145
SMAD2_HUMAN
379-427
49
2
A:379-427
C:379-427
49
49
1.12b
ENST00000262160
12b
ENSE00001949705
chr18:
45368321-45357922
10400
SMAD2_HUMAN
427-467
41
2
A:427-467
C:427-467
41
41
2.2a
ENST00000398417
2a
ENSE00001533125
chr18:
48573289-48573665
377
SMAD4_HUMAN
1-83
83
0
-
-
2.3
ENST00000398417
3
ENSE00000950229
chr18:
48575056-48575230
175
SMAD4_HUMAN
84-142
59
0
-
-
2.4
ENST00000398417
4
ENSE00000996859
chr18:
48575665-48575694
30
SMAD4_HUMAN
142-152
11
0
-
-
2.7
ENST00000398417
7
ENSE00000950230
chr18:
48581151-48581363
213
SMAD4_HUMAN
152-223
72
0
-
-
2.8
ENST00000398417
8
ENSE00000950231
chr18:
48584495-48584614
120
SMAD4_HUMAN
223-263
41
0
-
-
2.9
ENST00000398417
9
ENSE00000950232
chr18:
48584710-48584826
117
SMAD4_HUMAN
263-302
40
0
-
-
2.10
ENST00000398417
10
ENSE00000950233
chr18:
48586236-48586286
51
SMAD4_HUMAN
302-319
18
1
B:314-319
6
2.11
ENST00000398417
11
ENSE00000950234
chr18:
48591793-48591976
184
SMAD4_HUMAN
319-380
62
1
B:319-380
62
2.12
ENST00000398417
12
ENSE00000950235
chr18:
48593389-48593557
169
SMAD4_HUMAN
380-436
57
1
B:380-436
57
2.13
ENST00000398417
13
ENSE00000950236
chr18:
48603008-48603146
139
SMAD4_HUMAN
437-483
47
1
B:437-461
25
2.14b
ENST00000398417
14b
ENSE00001533123
chr18:
48604626-48611415
6790
SMAD4_HUMAN
483-552
70
1
B:490-549
60
[
close EXON info
]
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1u7va_ (A:)
1b: SCOP_d1u7vc_ (C:)
2a: SCOP_d1u7vb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SMAD/FHA domain
(62)
Superfamily
:
SMAD/FHA domain
(62)
Family
:
SMAD domain
(13)
Protein domain
:
Smad2 MH2 domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1u7va_
A:
1b
d1u7vc_
C:
Protein domain
:
Smad4 tumor suppressor C-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
2a
d1u7vb_
B:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1u7vA00 (A:270-466)
1b: CATH_1u7vB00 (B:314-549)
1c: CATH_1u7vC00 (C:272-466)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Tumour Suppressor Smad4
(52)
Homologous Superfamily
:
[code=2.60.200.10, no name defined]
(17)
Human (Homo sapiens)
(15)
1a
1u7vA00
A:270-466
1b
1u7vB00
B:314-549
1c
1u7vC00
C:272-466
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_MH2_1u7vC01 (C:272-445)
1b: PFAM_MH2_1u7vC02 (C:272-445)
1c: PFAM_MH2_1u7vB01 (B:317-532)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
SMAD-FHA
(27)
Family
:
MH2
(8)
Homo sapiens (Human)
(8)
1a
MH2-1u7vC01
C:272-445
1b
MH2-1u7vC02
C:272-445
1c
MH2-1u7vB01
B:317-532
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
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)
[
close Script example commands
]
Log
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (104 KB)
Header - Asym.Unit
Biol.Unit 1 (99 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1U7V
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help