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3KMZ
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (175 KB)
Biol.Unit 2 (174 KB)
Biol.Unit 3 (176 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RARALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH THE INVERSE AGONIST BMS493 AND A COREPRESSOR FRAGMENT
Authors
:
W. Bourguet, A. Le Maire
Date
:
11 Nov 09 (Deposition) - 02 Jun 10 (Release) - 14 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: B,C (2x)
Biol. Unit 3: A,D (2x)
Keywords
:
Nuclear Receptor Transcription Factor Ligand Binding Domain, Dna- Binding, Metal-Binding, Nucleus, Phosphoprotein, Proto-Oncogene, Receptor, Transcription, Transcription Regulation, Zinc-Finger, Chromatin Regulator, Repressor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Le Maire, C. Teyssier, C. Erb, M. Grimaldi, S. Alvarez, A. R. De Lera, P. Balaguer, H. Gronemeyer, C. A. Royer, P. Germain, W. Bourguet
A Unique Secondary-Structure Switch Controls Constitutive Gene Repression By Retinoic Acid Receptor.
Nat. Struct. Mol. Biol. V. 17 801 2010
[
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
2a: 4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLET... (EQOa)
2b: 4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLET... (EQOb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
2
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
EQO
2
Ligand/Ion
4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-2-YL]ETHENYL}BENZOIC ACID
3
GOL
9
Ligand/Ion
GLYCEROL
[
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]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH B:11 , PHE B:199 , PHE B:228 , SER B:232 , THR B:233 , CYS B:235 , ILE B:236 , LEU B:269 , ILE B:273 , ARG B:276 , PHE B:286 , SER B:287 , PHE B:302 , LEU C:2051 , HIS C:2054
BINDING SITE FOR RESIDUE EQO B 1
02
AC2
SOFTWARE
THR B:210 , ASN B:211 , ASN B:293 , GLN B:296 , HOH B:445
BINDING SITE FOR RESIDUE GOL B 422
03
AC3
SOFTWARE
THR B:210 , ASN B:212 , LEU B:224 , LYS B:227
BINDING SITE FOR RESIDUE GOL B 4
04
AC4
SOFTWARE
ALA B:263 , LEU B:266 , ASP B:267 , ARG B:385 , SER B:388 , HOH B:429 , HOH B:437
BINDING SITE FOR RESIDUE GOL B 5
05
AC5
SOFTWARE
LEU B:319 , GLU B:320 , GLU B:325 , VAL B:363 , ARG B:366 , ARG B:367 , ARG B:370 , MET B:373 , MET B:377
BINDING SITE FOR RESIDUE GOL B 9
06
AC6
SOFTWARE
HOH A:20 , PHE A:199 , TRP A:225 , PHE A:228 , SER A:232 , CYS A:235 , ILE A:236 , LEU A:269 , ILE A:273 , ARG A:276 , PHE A:286 , SER A:287 , PHE A:302 , LEU D:2051 , HIS D:2054
BINDING SITE FOR RESIDUE EQO A 2
07
AC7
SOFTWARE
LEU A:319 , GLU A:320 , GLU A:325 , VAL A:363 , ARG A:366 , ARG A:367 , ARG A:370 , MET A:373 , MET A:377
BINDING SITE FOR RESIDUE GOL A 422
08
AC8
SOFTWARE
HOH A:40 , LEU A:220 , GLY A:301 , ARG A:394 , ILE A:396 , THR A:397
BINDING SITE FOR RESIDUE GOL A 3
09
AC9
SOFTWARE
THR A:210 , ASN A:211 , SER A:214 , HOH A:423 , HOH A:469
BINDING SITE FOR RESIDUE GOL A 6
10
BC1
SOFTWARE
LYS A:360 , ARG A:364 , PRO A:371 , PHE A:374 , PRO A:375
BINDING SITE FOR RESIDUE GOL A 7
11
BC2
SOFTWARE
HOH A:54 , HOH A:88 , ALA A:263 , LEU A:266 , ASP A:267 , ARG A:385 , SER A:388 , ALA A:389
BINDING SITE FOR RESIDUE GOL A 8
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(5, 10)
Info
All Exons
Exon 1.10b (A:181-210 | B:181-210)
Exon 1.12b (A:211-269 | B:211-269)
Exon 1.13b (A:270-338 | B:270-338)
Exon 1.14 (A:338-391 | B:338-391)
Exon 1.15d (A:391-401 | B:391-401)
View:
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All Exon Boundaries
1: Boundary 1.8/1.10b
2: Boundary 1.10b/1.12b
3: Boundary 1.12b/1.13b
4: Boundary 1.13b/1.14
5: Boundary 1.14/1.15d
6: Boundary 1.15d/-
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
1.2
ENST00000394089
2
ENSE00001517476
chr17:
38474497-38474700
204
RARA_HUMAN
-
0
0
-
-
1.3
ENST00000394089
3
ENSE00001422265
chr17:
38487109-38487648
540
RARA_HUMAN
1-60
60
0
-
-
1.7
ENST00000394089
7
ENSE00001594260
chr17:
38504568-38504716
149
RARA_HUMAN
60-109
50
0
-
-
1.8
ENST00000394089
8
ENSE00001760241
chr17:
38506036-38506177
142
RARA_HUMAN
110-157
48
0
-
-
1.10b
ENST00000394089
10b
ENSE00000900551
chr17:
38508162-38508322
161
RARA_HUMAN
157-210
54
2
A:181-210
B:181-210
30
30
1.12b
ENST00000394089
12b
ENSE00000900554
chr17:
38508583-38508759
177
RARA_HUMAN
211-269
59
2
A:211-269
B:211-269
59
59
1.13b
ENST00000394089
13b
ENSE00001735102
chr17:
38510554-38510758
205
RARA_HUMAN
270-338
69
2
A:270-338
B:270-338
69
69
1.14
ENST00000394089
14
ENSE00000900558
chr17:
38511515-38511673
159
RARA_HUMAN
338-391
54
2
A:338-391
B:338-391
54
54
1.15d
ENST00000394089
15d
ENSE00001374856
chr17:
38512261-38513894
1634
RARA_HUMAN
391-462
72
2
A:391-401
B:391-401
11
11
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3kmzA00 (A:181-401)
1b: CATH_3kmzB00 (B:181-401)
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Classes
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)
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)
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
3kmzA00
A:181-401
1b
3kmzB00
B:181-401
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Hormone_recep_3kmzB01 (B:207-401)
1b: PFAM_Hormone_recep_3kmzB02 (B:207-401)
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Clans
(
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(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Hormone_recep]
(290)
Family
:
Hormone_recep
(290)
Homo sapiens (Human)
(244)
1a
Hormone_recep-3kmzB01
B:207-401
1b
Hormone_recep-3kmzB02
B:207-401
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Chain D
Asymmetric Unit 1
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Asym.Unit (183 KB)
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Biol.Unit 1 (175 KB)
Header - Biol.Unit 1
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