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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3W5K
Asym. Unit
Info
Asym.Unit (329 KB)
Biol.Unit 1 (322 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 SNAIL1 AND IMPORTIN BETA COMPLEX
Authors
:
S. Choi, E. Yamashita, N. Yasuhara, J. Song, S. Y. Son, Y. H. Won, Y. S. Shi T. Sekimoto, I. Y. Park, Y. Yoneda, S. J. Lee
Date
:
30 Jan 13 (Deposition) - 05 Mar 14 (Release) - 07 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Importin Beta, Nuclear Transport Factor Snail1, Transcription Repressor, Nuclear Protein-Metal Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Choi, E. Yamashita, N. Yasuhara, J. Song, S. Y. Son, Y. H. Won, H. R. Hong, Y. S. Shin, T. Sekimoto, I. Y. Park, Y. Yoneda, S. J. Lee
Structural Basis For The Selective Nuclear Import Of The C2H2 Zinc-Finger Protein Snail By Importin Beta.
Acta Crystallogr. , Sect. D V. 70 1050 2014
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS B:156 , CYS B:159 , LYS B:161 , HIS B:172 , HIS B:176
BINDING SITE FOR RESIDUE ZN B 501
2
AC2
SOFTWARE
CYS B:182 , THR B:184 , CYS B:185 , HIS B:198 , HIS B:202
BINDING SITE FOR RESIDUE ZN B 502
3
AC3
SOFTWARE
CYS B:210 , CYS B:213 , HIS B:226 , HIS B:230
BINDING SITE FOR RESIDUE ZN B 503
4
AC4
SOFTWARE
CYS B:238 , CYS B:241 , HIS B:254 , CYS B:259
BINDING SITE FOR RESIDUE ZN B 504
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: IMPORTIN_B_NT (A:21-101)
2: ZINC_FINGER_C2H2_1 (B:156-176|B:180-202|B:210-230)
3: HEAT_REPEAT (A:409-446)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IMPORTIN_B_NT
PS50166
Importin-beta N-terminal domain profile.
IMB1_HUMAN
21-101
1
A:21-101
2
ZINC_FINGER_C2H2_1
PS00028
Zinc finger C2H2 type domain signature.
SNAI1_HUMAN
156-176
180-202
210-230
3
B:156-176
B:180-202
B:210-230
3
HEAT_REPEAT
PS50077
HEAT repeat profile.
IMB1_HUMAN
409-446
1
A:409-446
[
close PROSITE info
]
Exons
(20, 20)
Info
All Exons
Exon 1.2 (A:15-33)
Exon 1.3 (A:34-94)
Exon 1.4 (A:95-161)
Exon 1.5 (A:162-212)
Exon 1.6 (A:213-232)
Exon 1.7 (A:233-262)
Exon 1.8 (A:263-299)
Exon 1.9 (A:300-333)
Exon 1.10 (A:334-408)
Exon 1.11 (A:409-472)
Exon 1.12 (A:473-516 (gaps))
Exon 1.13 (A:516-565)
Exon 1.14 (A:566-589)
Exon 1.15 (A:590-638)
Exon 1.16 (A:638-665)
Exon 1.17 (A:666-701)
Exon 1.18 (A:702-749)
Exon 1.19 (A:750-785)
Exon 1.20 (A:785-823)
Exon 1.21 (A:823-876)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
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 1.14/1.15
15: Boundary 1.15/1.16
16: Boundary 1.16/1.17
17: Boundary 1.17/1.18
18: Boundary 1.18/1.19
19: Boundary 1.19/1.20
20: Boundary 1.20/1.21
21: Boundary 1.21/1.22
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
ENST00000290158
1
ENSE00001328366
chr17:
45727275-45727650
376
IMB1_HUMAN
1-14
14
0
-
-
1.2
ENST00000290158
2
ENSE00001110328
chr17:
45727752-45727810
59
IMB1_HUMAN
14-33
20
1
A:15-33
19
1.3
ENST00000290158
3
ENSE00001043051
chr17:
45730060-45730242
183
IMB1_HUMAN
34-94
61
1
A:34-94
61
1.4
ENST00000290158
4
ENSE00000924979
chr17:
45734226-45734426
201
IMB1_HUMAN
95-161
67
1
A:95-161
67
1.5
ENST00000290158
5
ENSE00000924980
chr17:
45735874-45736026
153
IMB1_HUMAN
162-212
51
1
A:162-212
51
1.6
ENST00000290158
6
ENSE00000924981
chr17:
45738485-45738544
60
IMB1_HUMAN
213-232
20
1
A:213-232
20
1.7
ENST00000290158
7
ENSE00000924982
chr17:
45740455-45740544
90
IMB1_HUMAN
233-262
30
1
A:233-262
30
1.8
ENST00000290158
8
ENSE00000924983
chr17:
45741525-45741635
111
IMB1_HUMAN
263-299
37
1
A:263-299
37
1.9
ENST00000290158
9
ENSE00000924984
chr17:
45742423-45742524
102
IMB1_HUMAN
300-333
34
1
A:300-333
34
1.10
ENST00000290158
10
ENSE00000924985
chr17:
45745552-45745776
225
IMB1_HUMAN
334-408
75
1
A:334-408
75
1.11
ENST00000290158
11
ENSE00001043047
chr17:
45747044-45747235
192
IMB1_HUMAN
409-472
64
1
A:409-472
64
1.12
ENST00000290158
12
ENSE00000924987
chr17:
45748068-45748198
131
IMB1_HUMAN
473-516
44
1
A:473-516 (gaps)
44
1.13
ENST00000290158
13
ENSE00001043027
chr17:
45750384-45750531
148
IMB1_HUMAN
516-565
50
1
A:516-565
50
1.14
ENST00000290158
14
ENSE00000924989
chr17:
45750856-45750927
72
IMB1_HUMAN
566-589
24
1
A:566-589
24
1.15
ENST00000290158
15
ENSE00000924990
chr17:
45752004-45752148
145
IMB1_HUMAN
590-638
49
1
A:590-638
49
1.16
ENST00000290158
16
ENSE00000924991
chr17:
45753775-45753857
83
IMB1_HUMAN
638-665
28
1
A:638-665
28
1.17
ENST00000290158
17
ENSE00000924992
chr17:
45754386-45754493
108
IMB1_HUMAN
666-701
36
1
A:666-701
36
1.18
ENST00000290158
18
ENSE00000924993
chr17:
45755412-45755555
144
IMB1_HUMAN
702-749
48
1
A:702-749
48
1.19
ENST00000290158
19
ENSE00000924994
chr17:
45755674-45755779
106
IMB1_HUMAN
750-785
36
1
A:750-785
36
1.20
ENST00000290158
20
ENSE00000924995
chr17:
45757386-45757500
115
IMB1_HUMAN
785-823
39
1
A:785-823
39
1.21
ENST00000290158
21
ENSE00000924996
chr17:
45757874-45758035
162
IMB1_HUMAN
823-877
55
1
A:823-876
54
1.22
ENST00000290158
22
ENSE00001343442
chr17:
45759770-45760998
1229
IMB1_HUMAN
877-878
2
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3w5ka_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
ARM repeat
(317)
Family
:
Armadillo repeat
(77)
Protein domain
:
Importin beta
(14)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d3w5ka_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
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
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
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 (329 KB)
Header - Asym.Unit
Biol.Unit 1 (322 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
3W5K
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
