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.
1FM6
Biol. Unit 2
Info
Asym.Unit (186 KB)
Biol.Unit 1 (91 KB)
Biol.Unit 2 (91 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES.
Authors
:
R. T. Gampe Jr. , V. G. Montana, M. H. Lambert, A. B. Miller, R. K. Bledsoe M. V. Milburn, S. A. Kliewer, T. M. Willson, H. E. Xu
Date
:
16 Aug 00 (Deposition) - 16 Feb 01 (Release) - 26 Dec 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,D,E,U,V,X,Y
Biol. Unit 1: A,B,D,E (1x)
Biol. Unit 2: U,V,X,Y (1x)
Keywords
:
The Heterodimer Of The Nuclear Receptor Ligand Binding Domains Of Rxralpha And Ppargamma Bound Respectively With 9-Cis Retinoic Acid And Rosiglitazone And Co-Activator Peptides, Transcription
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. T. Gampe Jr. , V. G. Montana, M. H. Lambert, A. B. Miller, R. K. Bledsoe, M. V. Milburn, S. A. Kliewer, T. M. Willson, H. E. Xu
Asymmetry In The Ppargamma/Rxralpha Crystal Structure Reveals The Molecular Basis Of Heterodimerization Among Nuclear Receptors.
Mol. Cell V. 5 545 2000
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: (9CIS)-RETINOIC ACID (9CRa)
1b: (9CIS)-RETINOIC ACID (9CRb)
2a: 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(... (BRLa)
2b: 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(... (BRLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
9CR
1
Ligand/Ion
(9CIS)-RETINOIC ACID
2
BRL
1
Ligand/Ion
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ALA U:271 , PHE U:313 , ARG U:316 , LEU U:326 , ALA U:327 , CYS U:432 , HIS U:435
BINDING SITE FOR RESIDUE 9CR U 502
2
AC4
SOFTWARE
PHE X:282 , GLY X:284 , CYS X:285 , SER X:289 , HIS X:323 , TYR X:327 , MET X:364 , HIS X:449 , LEU X:453 , TYR X:473
BINDING SITE FOR RESIDUE BRL X 504
[
close Site info
]
SAPs(SNPs)/Variants
(11, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_014620 (P261L, chain U, )
02: VAR_010725 (Q286P, chain X, )
03: VAR_010726 (R288H, chain X, )
04: VAR_010727 (V290M, chain X, )
05: VAR_050582 (A327S, chain U, )
06: VAR_014621 (S336I, chain U, )
07: VAR_022700 (F360L, chain X, )
08: VAR_022701 (R397C, chain X, )
09: VAR_050583 (A398V, chain U, )
10: VAR_010728 (P467L, chain X, )
11: VAR_019772 (E685A, chain V/V/Y, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014620
P
261
L
RXRA_HUMAN
Polymorphism
2234960
U
P
261
L
02
UniProt
VAR_010725
Q
314
P
PPARG_HUMAN
Unclassified
28936407
X
Q
286
P
03
UniProt
VAR_010726
R
316
H
PPARG_HUMAN
Unclassified
28936407
X
R
288
H
04
UniProt
VAR_010727
V
318
M
PPARG_HUMAN
Unclassified
---
X
V
290
M
05
UniProt
VAR_050582
A
327
S
RXRA_HUMAN
Polymorphism
1805345
U
A
327
S
06
UniProt
VAR_014621
S
336
I
RXRA_HUMAN
Polymorphism
1805345
U
S
336
I
07
UniProt
VAR_022700
F
388
L
PPARG_HUMAN
Disease (FPLD3)
---
X
F
360
L
08
UniProt
VAR_022701
R
425
C
PPARG_HUMAN
Disease (FPLD3)
---
X
R
397
C
09
UniProt
VAR_050583
A
398
V
RXRA_HUMAN
Polymorphism
11542209
U
A
398
V
10
UniProt
VAR_010728
P
495
L
PPARG_HUMAN
Unclassified
---
X
P
467
L
11
UniProt
VAR_019772
E
685
A
NCOA1_HUMAN
Polymorphism
1049021
V
V/Y
E
628
685
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1fm6d_ (D:)
1b: SCOP_d1fm6x_ (X:)
2a: SCOP_d1fm6a_ (A:)
2b: SCOP_d1fm6u_ (U:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Nuclear receptor ligand-binding domain
(609)
Superfamily
:
Nuclear receptor ligand-binding domain
(609)
Family
:
Nuclear receptor ligand-binding domain
(598)
Protein domain
:
Peroxisome proliferator activated receptor gamma, PPAR-gamma
(83)
Human (Homo sapiens) [TaxId: 9606]
(83)
1a
d1fm6d_
D:
1b
d1fm6x_
X:
Protein domain
:
Retinoid-X receptor alpha (RXR-alpha)
(36)
Human (Homo sapiens) [TaxId: 9606]
(33)
2a
d1fm6a_
A:
2b
d1fm6u_
U:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1fm6A00 (A:227-458)
1b: CATH_1fm6U00 (U:227-458)
1c: CATH_1fm6D00 (D:206-477)
1d: CATH_1fm6X00 (X:206-477)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Retinoid X Receptor
(409)
Homologous Superfamily
:
Retinoid X Receptor
(409)
Human (Homo sapiens)
(337)
1a
1fm6A00
A:227-458
1b
1fm6U00
U:227-458
1c
1fm6D00
D:206-477
1d
1fm6X00
X:206-477
[
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 U
Chain V
Chain X
Chain Y
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 (186 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
Biol.Unit 2 (91 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
1FM6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
