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.
2RQB
Asym. Unit
Info
Asym.Unit (855 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
SOLUTION STRUCTURE OF MDA5 CTD
Authors
:
K. Takahasi, H. Kumeta, N. Tsuduki, R. Narita, T. Shigemoto, R. Hirai, M. Yoneyama, M. Horiuchi, K. Ogura, T. Fujita, I. Fuyuhiko
Date
:
17 Mar 09 (Deposition) - 05 May 09 (Release) - 07 Jul 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Rna Binding Protein, Hydrolase, Alternative Splicing, Antiviral Defense, Atp-Binding, Cytoplasm, Diabetes Mellitus, Helicase, Host-Virus Interaction, Immune Response, Innate Immunity, Nucleotide-Binding, Nucleus, Phosphoprotein, Polymorphism, Rna-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Takahasi, H. Kumeta, N. Tsuduki, R. Narita, T. Shigemoto, R. Hirai, M. Yoneyama, M. Horiuchi, K. Ogura, T. Fujita, F. Inagaki
Solution Structures Of Cytosolic Rna Sensor Mda5 And Lgp2 C-Terminal Domains: Identification Of The Rna Recognition Loop In Rig-I-Like Receptors
J. Biol. Chem. V. 284 17465 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:907 , CYS A:910 , CYS A:962 , CYS A:964
BINDING SITE FOR RESIDUE ZN A 1026
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_021595 (A946T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021595
A
946
T
IFIH1_HUMAN
Polymorphism
1990760
A
A
946
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RLR_CTR (A:896-1020)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RLR_CTR
PS51789
RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile.
IFIH1_HUMAN
893-1020
1
A:896-1020
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.13 (A:891-895)
Exon 1.14 (A:896-936)
Exon 1.15 (A:936-966)
Exon 1.16 (A:967-1025)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.12/1.13
2: Boundary 1.13/1.14
3: Boundary 1.14/1.15
4: Boundary 1.15/1.16
5: Boundary 1.16/-
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
1.1a
ENST00000263642
1a
ENSE00001858759
chr2:
163175213-163174365
849
IFIH1_HUMAN
1-151
151
0
-
-
1.2a
ENST00000263642
2a
ENSE00000840792
chr2:
163167443-163167275
169
IFIH1_HUMAN
152-208
57
0
-
-
1.3b
ENST00000263642
3b
ENSE00000840791
chr2:
163163365-163163219
147
IFIH1_HUMAN
208-257
50
0
-
-
1.4
ENST00000263642
4
ENSE00000840790
chr2:
163150178-163150074
105
IFIH1_HUMAN
257-292
36
0
-
-
1.5
ENST00000263642
5
ENSE00000840789
chr2:
163144865-163144645
221
IFIH1_HUMAN
292-365
74
0
-
-
1.6
ENST00000263642
6
ENSE00000840788
chr2:
163139086-163138876
211
IFIH1_HUMAN
366-436
71
0
-
-
1.7
ENST00000263642
7
ENSE00001073453
chr2:
163138055-163137838
218
IFIH1_HUMAN
436-508
73
0
-
-
1.8
ENST00000263642
8
ENSE00001073457
chr2:
163136622-163136506
117
IFIH1_HUMAN
509-547
39
0
-
-
1.9
ENST00000263642
9
ENSE00001073451
chr2:
163134838-163134715
124
IFIH1_HUMAN
548-589
42
0
-
-
1.10
ENST00000263642
10
ENSE00001073449
chr2:
163134203-163133925
279
IFIH1_HUMAN
589-682
94
0
-
-
1.11
ENST00000263642
11
ENSE00001073452
chr2:
163133456-163133197
260
IFIH1_HUMAN
682-768
87
0
-
-
1.12
ENST00000263642
12
ENSE00001073458
chr2:
163130454-163130305
150
IFIH1_HUMAN
769-818
50
0
-
-
1.13
ENST00000263642
13
ENSE00001073450
chr2:
163128897-163128736
162
IFIH1_HUMAN
819-872
54
1
A:891-895
5
1.14
ENST00000263642
14
ENSE00001073448
chr2:
163124787-163124597
191
IFIH1_HUMAN
873-936
64
1
A:896-936
41
1.15
ENST00000263642
15
ENSE00001073454
chr2:
163124079-163123989
91
IFIH1_HUMAN
936-966
31
1
A:936-966
31
1.16
ENST00000263642
16
ENSE00001073456
chr2:
163123889-163123589
301
IFIH1_HUMAN
967-1025
59
1
A:967-1025
59
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2rqba_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Mss4-like
(27)
Superfamily
:
RIG-I C-terminal-like
(10)
Family
:
RIG-I C-terminal domain-like
(9)
Protein domain
:
MDA5 C-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2rqba_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_RIG_I_C_RD_2rqbA01 (A:901-1022)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RIG-I_C-RD]
(10)
Family
:
RIG-I_C-RD
(10)
Homo sapiens (Human)
(10)
1a
RIG-I_C-RD-2rqbA01
A:901-1022
[
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
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 (855 KB)
Header - Asym.Unit
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
2RQB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help