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1MR1
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (50 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A SMAD4-SKI COMPLEX
Authors
:
J. -W. Wu, A. R. Krawitz, J. Chai, W. Li, F. Zhang, K. Luo, Y. Shi
Date
:
17 Sep 02 (Deposition) - 21 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Smad, Ski, Cancer, Tgf-B Signaling, Protein Interaction, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. -W. Wu, A. R. Krawitz, J. Chai, W. Li, F. Zhang, K. Luo, Y. Shi
Structural Mechanism Of Smad4 Recognition By The Nuclear Oncoprotein Ski: Insights On Ski-Mediated Repression Of Tgf-Beta Signaling
Cell(Cambridge, Mass. ) V. 111 357 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
2
Ligand/Ion
ZINC ION
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS C:247 , CYS C:250 , HIS C:262 , HIS C:264
BINDING SITE FOR RESIDUE ZN C 601
2
AC2
SOFTWARE
CYS D:247 , CYS D:250 , HIS D:262 , HIS D:264
BINDING SITE FOR RESIDUE ZN D 602
[
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]
SAPs(SNPs)/Variants
(12, 24)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_022833 (E330G, chain A/B, )
02: VAR_036476 (D351N, chain A/B, )
03: VAR_SMAD4_HUMAN_CCDS11950_1_02 (D351N, chain A/B, )
04: VAR_019571 (G352R, chain A/B, )
05: VAR_019572 (R361C, chain A/B, )
06: VAR_036477 (R361H, chain A/B, )
07: VAR_SMAD4_HUMAN_CCDS11950_1_03 (R361H, chain A/B, )
08: VAR_019573 (G386D, chain A/B, )
09: VAR_011380 (D493H, chain A/B, )
10: VAR_067602 (I500M, chain A/B, )
11: VAR_067603 (I500T, chain A/B, )
12: VAR_067604 (I500V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_022833
E
330
G
SMAD4_HUMAN
Disease (JPS)
281875324
A/B
E
330
G
02
UniProt
VAR_036476
D
351
N
SMAD4_HUMAN
Unclassified
---
A/B
D
351
N
03
CancerSNP
VAR_SMAD4_HUMAN_CCDS11950_1_02
*
D
351
N
SMAD4_HUMAN
Disease (Colorectal cancer)
---
A/B
D
351
N
04
UniProt
VAR_019571
G
352
R
SMAD4_HUMAN
Disease (JPS)
121912581
A/B
G
352
R
05
UniProt
VAR_019572
R
361
C
SMAD4_HUMAN
Disease (JPS)
80338963
A/B
R
361
C
06
UniProt
VAR_036477
R
361
H
SMAD4_HUMAN
Unclassified
---
A/B
R
361
H
07
CancerSNP
VAR_SMAD4_HUMAN_CCDS11950_1_03
*
R
361
H
SMAD4_HUMAN
Disease (Colorectal cancer)
---
A/B
R
361
H
08
UniProt
VAR_019573
G
386
D
SMAD4_HUMAN
Disease (JP/HHT)
28936393
A/B
G
386
D
09
UniProt
VAR_011380
D
493
H
SMAD4_HUMAN
Unclassified
28936392
A/B
D
493
H
10
UniProt
VAR_067602
I
500
M
SMAD4_HUMAN
Disease (MYHRS)
281875320
A/B
I
500
M
11
UniProt
VAR_067603
I
500
T
SMAD4_HUMAN
Disease (MYHRS)
281875321
A/B
I
500
T
12
UniProt
VAR_067604
I
500
V
SMAD4_HUMAN
Disease (MYHRS)
281875322
A/B
I
500
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MH2 (A:323-543,B:323-550)
;
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.
SMAD4_HUMAN
323-552
2
A:323-543
B:323-550
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.1 (C:216-312 | D:217-312)
Exon 2.10 (A:319-319 | B:319-319)
Exon 2.11 (A:319-380 | B:319-380)
Exon 2.12 (A:380-436 | B:380-436)
Exon 2.13 (A:437-461 | B:437-452)
Exon 2.14b (A:492-543 | B:492-550)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.4b
3: Boundary 2.9/2.10
4: Boundary 2.10/2.11
5: Boundary 2.11/2.12
6: Boundary 2.12/2.13
7: Boundary 2.13/2.14b
8: 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
1.1
ENST00000378536
1
ENSE00001477855
chr1:
2160134-2161174
1041
SKI_HUMAN
1-323
323
2
C:216-312
D:217-312
97
96
1.4b
ENST00000378536
4b
ENSE00001035938
chr1:
2234417-2234542
126
SKI_HUMAN
324-365
42
0
-
-
1.5b
ENST00000378536
5b
ENSE00001035943
chr1:
2234724-2234839
116
SKI_HUMAN
366-404
39
0
-
-
1.6b
ENST00000378536
6b
ENSE00001035948
chr1:
2235279-2235541
263
SKI_HUMAN
404-492
89
0
-
-
1.7b
ENST00000378536
7b
ENSE00001035949
chr1:
2235732-2236024
293
SKI_HUMAN
492-589
98
0
-
-
1.8
ENST00000378536
8
ENSE00001035950
chr1:
2237459-2237689
231
SKI_HUMAN
590-666
77
0
-
-
1.9
ENST00000378536
9
ENSE00001477851
chr1:
2238016-2241558
3543
SKI_HUMAN
667-728
62
0
-
-
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
2
A:319-319
B:319-319
1
1
2.11
ENST00000398417
11
ENSE00000950234
chr18:
48591793-48591976
184
SMAD4_HUMAN
319-380
62
2
A:319-380
B:319-380
62
62
2.12
ENST00000398417
12
ENSE00000950235
chr18:
48593389-48593557
169
SMAD4_HUMAN
380-436
57
2
A:380-436
B:380-436
57
57
2.13
ENST00000398417
13
ENSE00000950236
chr18:
48603008-48603146
139
SMAD4_HUMAN
437-483
47
2
A:437-461
B:437-452
25
16
2.14b
ENST00000398417
14b
ENSE00001533123
chr18:
48604626-48611415
6790
SMAD4_HUMAN
483-552
70
2
A:492-543
B:492-550
52
59
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1mr1a_ (A:)
1b: SCOP_d1mr1b_ (B:)
2a: SCOP_d1mr1c_ (C:)
2b: SCOP_d1mr1d_ (D:)
View:
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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
:
Smad4 tumor suppressor C-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1mr1a_
A:
1b
d1mr1b_
B:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
SAND domain-like
(4)
Superfamily
:
SAND domain-like
(4)
Family
:
SMAD4-binding domain of oncoprotein Ski
(1)
Protein domain
:
SMAD4-binding domain of oncoprotein Ski
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1mr1c_
C:
2b
d1mr1d_
D:
[
close SCOP info
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1mr1D00 (D:217-312)
1b: CATH_1mr1C00 (C:216-312)
2a: CATH_1mr1A00 (A:319-543)
2b: CATH_1mr1B00 (B:319-550)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
SAND domain
(4)
Homologous Superfamily
:
SAND domain
(4)
Human (Homo sapiens)
(3)
1a
1mr1D00
D:217-312
1b
1mr1C00
C:216-312
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)
2a
1mr1A00
A:319-543
2b
1mr1B00
B:319-550
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_MH2_1mr1B01 (B:319-532)
1b: PFAM_MH2_1mr1B02 (B:319-532)
2a: PFAM_c_SKI_SMAD_bind_1mr1D01 (D:219-312)
2b: PFAM_c_SKI_SMAD_bind_1mr1D02 (D:219-312)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
SMAD-FHA
(27)
Family
:
MH2
(8)
Homo sapiens (Human)
(8)
1a
MH2-1mr1B01
B:319-532
1b
MH2-1mr1B02
B:319-532
Clan
:
no clan defined [family: c-SKI_SMAD_bind]
(1)
Family
:
c-SKI_SMAD_bind
(1)
Homo sapiens (Human)
(1)
2a
c-SKI_SMAD_bind-1mr1D01
D:219-312
2b
c-SKI_SMAD_bind-1mr1D02
D:219-312
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