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.
1YA0
Asym. Unit
Info
Asym.Unit (166 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 2 (82 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 N-TERMINAL DOMAIN OF HUMAN SMG7
Authors
:
N. Fukuhara, J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, E. Conti
Date
:
17 Dec 04 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Alpha-Helical Repeat, Tetratricopetide Repeat (Tpr), 14-3-3, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Fukuhara, J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, E. Conti
Smg7 Is A 14-3-3-Like Adaptor In The Nonsense-Mediated Mrna Decay Pathway.
Mol. Cell V. 17 537 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:66 , ARG A:163 , TYR A:164
BINDING SITE FOR RESIDUE SO4 A 498
2
AC2
SOFTWARE
LYS B:66 , ARG B:163 , TYR B:164 , HOH B:669
BINDING SITE FOR RESIDUE SO4 B 498
3
AC3
SOFTWARE
SER B:184 , GLY B:423 , ARG B:428 , HOH B:581
BINDING SITE FOR RESIDUE SO4 B 499
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(14, 28)
Info
All Exons
Exon 1.1e (A:1-10 | B:1-10)
Exon 1.6a (A:10-21 | B:10-21)
Exon 1.7b (A:21-60 | B:21-60)
Exon 1.8b (A:60-104 | B:60-104)
Exon 1.10c (A:105-162 (gaps) | B:105-162 (gaps...)
Exon 1.12 (A:162-186 | B:162-186)
Exon 1.13b (A:186-236 | B:186-236)
Exon 1.14b (A:236-281 | B:236-281)
Exon 1.15 (A:282-336 | B:282-336)
Exon 1.16 (A:336-388 (gaps) | B:336-388 (gaps...)
Exon 1.17 (A:388-412 (gaps) | B:388-412)
Exon 1.18 (A:412-432 | B:412-432)
Exon 1.19 (A:432-472 (gaps) | B:432-472 (gaps...)
Exon 1.20b (A:472-497 | B:472-497)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1e
02: Boundary 1.1e/1.6a
03: Boundary 1.6a/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.10c
06: Boundary 1.10c/1.12
07: Boundary 1.12/1.13b
08: Boundary 1.13b/1.14b
09: Boundary 1.14b/1.15
10: Boundary 1.15/1.16
11: Boundary 1.16/1.17
12: Boundary 1.17/1.18
13: Boundary 1.18/1.19
14: Boundary 1.19/1.20b
15: Boundary 1.20b/1.21
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
1.1e
ENST00000347615
1e
ENSE00002181443
chr1:
183441637-183441784
148
SMG7_HUMAN
1-10
10
2
A:1-10
B:1-10
10
10
1.6a
ENST00000347615
6a
ENSE00001675624
chr1:
183481972-183482003
32
SMG7_HUMAN
10-21
12
2
A:10-21
B:10-21
12
12
1.7b
ENST00000347615
7b
ENSE00002159151
chr1:
183485009-183485126
118
SMG7_HUMAN
21-60
40
2
A:21-60
B:21-60
40
40
1.8b
ENST00000347615
8b
ENSE00001067886
chr1:
183486823-183486955
133
SMG7_HUMAN
60-104
45
2
A:60-104
B:60-104
45
45
1.10c
ENST00000347615
10c
ENSE00001067882
chr1:
183495731-183495902
172
SMG7_HUMAN
105-162
58
2
A:105-162 (gaps)
B:105-162 (gaps)
58
58
1.12
ENST00000347615
12
ENSE00002188851
chr1:
183497091-183497162
72
SMG7_HUMAN
162-186
25
2
A:162-186
B:162-186
25
25
1.13b
ENST00000347615
13b
ENSE00001607532
chr1:
183498027-183498177
151
SMG7_HUMAN
186-236
51
2
A:186-236
B:186-236
51
51
1.14b
ENST00000347615
14b
ENSE00001598042
chr1:
183498533-183498668
136
SMG7_HUMAN
236-281
46
2
A:236-281
B:236-281
46
46
1.15
ENST00000347615
15
ENSE00001743469
chr1:
183502299-183502461
163
SMG7_HUMAN
282-336
55
2
A:282-336
B:282-336
55
55
1.16
ENST00000347615
16
ENSE00001723317
chr1:
183502811-183502967
157
SMG7_HUMAN
336-388
53
2
A:336-388 (gaps)
B:336-388 (gaps)
53
53
1.17
ENST00000347615
17
ENSE00001766732
chr1:
183506280-183506350
71
SMG7_HUMAN
388-412
25
2
A:388-412 (gaps)
B:388-412
25
25
1.18
ENST00000347615
18
ENSE00001664594
chr1:
183507515-183507575
61
SMG7_HUMAN
412-432
21
2
A:412-432
B:412-432
21
21
1.19
ENST00000347615
19
ENSE00001627281
chr1:
183510119-183510238
120
SMG7_HUMAN
432-472
41
2
A:432-472 (gaps)
B:432-472 (gaps)
41
41
1.20b
ENST00000347615
20b
ENSE00001264233
chr1:
183511211-183511637
427
SMG7_HUMAN
472-614
143
2
A:472-497
B:472-497
26
26
1.21
ENST00000347615
21
ENSE00001744227
chr1:
183513488-183513632
145
SMG7_HUMAN
615-663
49
0
-
-
1.22
ENST00000347615
22
ENSE00001696991
chr1:
183514065-183514447
383
SMG7_HUMAN
663-790
128
0
-
-
1.23c
ENST00000347615
23c
ENSE00001067890
chr1:
183515101-183515472
372
SMG7_HUMAN
791-914
124
0
-
-
1.25b
ENST00000347615
25b
ENSE00000774233
chr1:
183518343-183518423
81
SMG7_HUMAN
915-941
27
0
-
-
1.26a
ENST00000347615
26a
ENSE00000774234
chr1:
183518899-183519058
160
SMG7_HUMAN
942-995
54
0
-
-
1.27a
ENST00000347615
27a
ENSE00000774235
chr1:
183519886-183520056
171
SMG7_HUMAN
995-1052
58
0
-
-
1.28
ENST00000347615
28
ENSE00000774236
chr1:
183520180-183520325
146
SMG7_HUMAN
1052-1100
49
0
-
-
1.29b
ENST00000347615
29b
ENSE00001822143
chr1:
183520953-183523321
2369
SMG7_HUMAN
1101-1137
37
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ya0b_ (B:)
2a: SCOP_d1ya0a1 (A:1-497)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
TPR-like
(83)
Family
:
Tetratricopeptide repeat (TPR)
(47)
Protein domain
:
automated matches
(11)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d1ya0b_
B:
Protein domain
:
SMG-7
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1ya0a1
A:1-497
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_EST1_DNA_bind_1ya0B01 (B:171-431)
1b: PFAM_EST1_DNA_bind_1ya0B02 (B:171-431)
2a: PFAM_EST1_1ya0B03 (B:52-172)
2b: PFAM_EST1_1ya0B04 (B:52-172)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TPR
(230)
Family
:
EST1_DNA_bind
(1)
Homo sapiens (Human)
(1)
1a
EST1_DNA_bind-1ya0B01
B:171-431
1b
EST1_DNA_bind-1ya0B02
B:171-431
Clan
:
no clan defined [family: EST1]
(1)
Family
:
EST1
(1)
Homo sapiens (Human)
(1)
2a
EST1-1ya0B03
B:52-172
2b
EST1-1ya0B04
B:52-172
[
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 (166 KB)
Header - Asym.Unit
Biol.Unit 1 (80 KB)
Header - Biol.Unit 1
Biol.Unit 2 (82 KB)
Header - Biol.Unit 2
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
1YA0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
