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1F88
Asym. Unit
Info
Asym.Unit (115 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (53 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE RHODOPSIN
Authors
:
T. Okada, K. Palczewski, R. E. Stenkamp, M. Miyano
Date
:
29 Jun 00 (Deposition) - 04 Aug 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Keywords
:
Photoreceptor, G Protein-Coupled Receptor, Membrane Protein, Retinal Protein, Visual Pigment, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Palczewski, T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima, B. A. Fox, I. Le Trong, D. C. Teller, T. Okada, R. E. Stenkamp, M. Yamamoto, M. Miyano
Crystal Structure Of Rhodopsin: A G Protein-Coupled Receptor.
Science V. 289 739 2000
[
close entry info
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Hetero Components
(5, 21)
Info
All Hetero Components
1a: MERCURY (II) ION (HGa)
1b: MERCURY (II) ION (HGb)
1c: MERCURY (II) ION (HGc)
1d: MERCURY (II) ION (HGd)
1e: MERCURY (II) ION (HGe)
1f: MERCURY (II) ION (HGf)
2a: ALPHA-D-MANNOSE (MANa)
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: RETINAL (RETa)
4b: RETINAL (RETb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HG
6
Ligand/Ion
MERCURY (II) ION
2
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
RET
2
Ligand/Ion
RETINAL
5
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:4 , ASN A:15 , GLY A:18 , VAL A:20 , ARG A:21 , NAG A:502 , LYS B:16 , NAG B:601
BINDING SITE FOR RESIDUE NAG A 501
02
AC2
SOFTWARE
ARG A:21 , NAG A:501 , LYS B:16
BINDING SITE FOR RESIDUE NAG A 502
03
AC3
SOFTWARE
NAG A:501 , THR B:4 , ASN B:15 , GLY B:18 , VAL B:20 , ARG B:21 , NAG B:602
BINDING SITE FOR RESIDUE NAG B 601
04
AC4
SOFTWARE
LYS A:16 , ARG B:21 , NAG B:601 , MAN B:603
BINDING SITE FOR RESIDUE NAG B 602
05
AC5
SOFTWARE
NAG B:602
BINDING SITE FOR RESIDUE MAN B 603
06
AC6
SOFTWARE
MET A:1 , ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:702 , HOH A:953 , ZN B:909
BINDING SITE FOR RESIDUE NAG A 701
07
AC7
SOFTWARE
NAG A:701
BINDING SITE FOR RESIDUE NAG A 702
08
AC8
SOFTWARE
ASN B:2 , GLY B:280 , SER B:281 , ASP B:282 , NAG B:802
BINDING SITE FOR RESIDUE NAG B 801
09
AC9
SOFTWARE
NAG B:801
BINDING SITE FOR RESIDUE NAG B 802
10
BC1
SOFTWARE
CYS A:264 , THR A:297
BINDING SITE FOR RESIDUE HG A 901
11
BC2
SOFTWARE
ALA B:260 , CYS B:264 , THR B:297
BINDING SITE FOR RESIDUE HG B 902
12
BC3
SOFTWARE
ALA A:132 , CYS A:222 , TYR A:223 , LEU A:226
BINDING SITE FOR RESIDUE HG A 903
13
BC4
SOFTWARE
ALA B:132 , CYS B:222 , TYR B:223 , LEU B:226
BINDING SITE FOR RESIDUE HG B 904
14
BC5
SOFTWARE
GLN A:312 , CYS A:316 , SER A:338
BINDING SITE FOR RESIDUE HG A 905
15
BC6
SOFTWARE
HIS B:65 , CYS B:316
BINDING SITE FOR RESIDUE HG B 906
16
BC7
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 907
17
BC8
SOFTWARE
GLU A:196 , PHE B:276 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 908
18
BC9
SOFTWARE
NAG A:701 , PRO B:7 , HIS B:195
BINDING SITE FOR RESIDUE ZN B 909
19
CC1
SOFTWARE
LYS A:311 , ARG A:314
BINDING SITE FOR RESIDUE ZN A 910
20
CC2
SOFTWARE
ALA A:117 , THR A:118 , GLY A:121 , GLU A:122 , SER A:186 , CYS A:187 , MET A:207 , PHE A:212 , TRP A:265 , TYR A:268 , ALA A:269 , ALA A:292 , LYS A:296
BINDING SITE FOR RESIDUE RET A 977
21
CC3
SOFTWARE
ALA B:117 , THR B:118 , GLY B:121 , GLU B:122 , CYS B:187 , ILE B:189 , MET B:207 , PHE B:212 , PHE B:261 , TYR B:268 , ALA B:269 , ALA B:292 , LYS B:296
BINDING SITE FOR RESIDUE RET B 978
[
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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:
Select:
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
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.1 (A:1-124 | B:1-124)
Exon 1.2 (A:124-180 | B:124-180 (gaps))
Exon 1.3 (A:180-235 | B:180-226)
Exon 1.4 (A:240-315 | B:243-315)
Exon 1.5 (A:316-348 (gaps) | B:316-326)
View:
Select:
Label:
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 (gaps)
57
57
1.3
ENSBTAT00000001730
3
ENSBTAE00000013844
chr22:
57730259-57730094
166
OPSD_BOVIN
180-235
56
2
A:180-235
B:180-226
56
47
1.4
ENSBTAT00000001730
4
ENSBTAE00000013845
chr22:
57729975-57729736
240
OPSD_BOVIN
236-315
80
2
A:240-315
B:243-315
76
73
1.5
ENSBTAT00000001730
5
ENSBTAE00000326840
chr22:
57728876-57728766
111
OPSD_BOVIN
316-351
36
2
A:316-348 (gaps)
B:316-326
33
11
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1f88a_ (A:)
1b: SCOP_d1f88b_ (B:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Rhodopsin
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d1f88a_
A:
1b
d1f88b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1f88B00 (B:1-326)
1b: CATH_1f88A00 (A:1-348)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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)
Cattle (Bos taurus)
(9)
1a
1f88B00
B:1-326
1b
1f88A00
A:1-348
[
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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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Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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