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3CAP
Asym. Unit
Info
Asym.Unit (120 KB)
Biol.Unit 1 (113 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NATIVE OPSIN: THE G PROTEIN-COUPLED RECEPTOR RHODOPSIN IN ITS LIGAND-FREE STATE
Authors
:
J. H. Park, P. Scheerer, K. P. Hofmann, H. -W. Choe, O. P. Ernst
Date
:
20 Feb 08 (Deposition) - 24 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
G Protein-Coupled Receptor, Opsin, Rhodopsin, Membrane Protein, Retinal Protein, Photoreceptor, Ligand-Free State, Chromophore, G- Protein Coupled Receptor, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein, Photoreceptor Protein, Sensory Transduction, Transducer, Transmembrane, Vision, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Park, P. Scheerer, K. P. Hofmann, H. -W. Choe, O. P. Ernst
Crystal Structure Of The Ligand-Free G-Protein-Coupled Receptor Opsin
Nature V. 454 183 2008
[
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: B-2-OCTYLGLUCOSIDE (BGLa)
1b: B-2-OCTYLGLUCOSIDE (BGLb)
1c: B-2-OCTYLGLUCOSIDE (BGLc)
1d: B-2-OCTYLGLUCOSIDE (BGLd)
1e: B-2-OCTYLGLUCOSIDE (BGLe)
1f: B-2-OCTYLGLUCOSIDE (BGLf)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4a: PALMITIC ACID (PLMa)
4b: PALMITIC ACID (PLMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGL
6
Ligand/Ion
B-2-OCTYLGLUCOSIDE
2
BMA
4
Ligand/Ion
BETA-D-MANNOSE
3
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PLM
2
Ligand/Ion
PALMITIC ACID
[
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Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:4 , ASN A:15 , GLY A:18
BINDING SITE FOR RESIDUE NAG A 401
02
AC2
SOFTWARE
ARG A:21
BINDING SITE FOR RESIDUE NAG A 402
03
AC4
SOFTWARE
ASN B:15 , GLY B:18
BINDING SITE FOR RESIDUE NAG B 501
04
AC5
SOFTWARE
ARG B:21
BINDING SITE FOR RESIDUE NAG B 502
05
AC7
SOFTWARE
GLU A:25
BINDING SITE FOR RESIDUE BMA B 504
06
AC8
SOFTWARE
MET A:1 , ASN A:2 , GLY A:280 , ASP A:282
BINDING SITE FOR RESIDUE NAG A 601
07
AC9
SOFTWARE
MET A:1 , MET B:1 , ASN B:2 , GLY B:280
BINDING SITE FOR RESIDUE NAG B 701
08
BC1
SOFTWARE
GLU A:33 , TRP A:35 , GLN A:36
BINDING SITE FOR RESIDUE BGL A 802
09
BC2
SOFTWARE
PHE A:220 , LYS A:231 , THR A:251
BINDING SITE FOR RESIDUE BGL A 803
10
BC3
SOFTWARE
HIS A:100 , TRP B:35
BINDING SITE FOR RESIDUE BGL A 804
11
BC4
SOFTWARE
TRP A:35 , TYR B:96 , HIS B:100
BINDING SITE FOR RESIDUE BGL B 805
12
BC5
SOFTWARE
LEU A:321 , CYS A:322 , THR B:297 , TYR B:301 , MET B:309
BINDING SITE FOR RESIDUE PLM A 901
13
BC6
SOFTWARE
ILE A:256 , THR A:297 , TYR A:301 , CYS B:322
BINDING SITE FOR RESIDUE PLM B 902
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:123-139,B:123-139)
2: OPSIN (A:290-306,B:290-306)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_PROTEIN_RECEP_F1_1
PS00237
G-protein coupled receptors family 1 signature.
OPSD_BOVIN
123-139
2
A:123-139
B:123-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
2
A:290-306
B:290-306
[
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]
Exons
(5, 10)
Info
All Exons
Exon 1.1 (A:1-124 | B:1-124)
Exon 1.2 (A:124-180 | B:124-180)
Exon 1.3 (A:180-235 | B:180-235)
Exon 1.4 (A:236-315 | B:236-315)
Exon 1.5 (A:316-326 | B:316-326)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
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
ENSBTAT00000001730
1
ENSBTAE00000013842
chr22:
57733705-57733336
370
OPSD_BOVIN
1-124
124
2
A:1-124
B:1-124
124
124
1.2
ENSBTAT00000001730
2
ENSBTAE00000013843
chr22:
57731646-57731478
169
OPSD_BOVIN
124-180
57
2
A:124-180
B:124-180
57
57
1.3
ENSBTAT00000001730
3
ENSBTAE00000013844
chr22:
57730259-57730094
166
OPSD_BOVIN
180-235
56
2
A:180-235
B:180-235
56
56
1.4
ENSBTAT00000001730
4
ENSBTAE00000013845
chr22:
57729975-57729736
240
OPSD_BOVIN
236-315
80
2
A:236-315
B:236-315
80
80
1.5
ENSBTAT00000001730
5
ENSBTAE00000326840
chr22:
57728876-57728766
111
OPSD_BOVIN
316-351
36
2
A:316-326
B:316-326
11
11
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3capa_ (A:)
1b: SCOP_d3capb_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Family A G protein-coupled receptor-like
(138)
Superfamily
:
Family A G protein-coupled receptor-like
(138)
Family
:
Rhodopsin-like
(16)
Protein domain
:
automated matches
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d3capa_
A:
1b
d3capb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3capA00 (A:1-326)
1b: CATH_3capB00 (B:1-326)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Bovine (Bos taurus)
(4)
1a
3capA00
A:1-326
1b
3capB00
B:1-326
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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