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2ZIY
Asym. Unit
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Asym.Unit (60 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SQUID RHODOPSIN
Authors
:
M. Miyano, T. Shimamura
Date
:
27 Feb 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Transmembrane Helices, Chromophore, G-Protein Coupled Receptor, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein, Photoreceptor Protein, Receptor, Retinal Protein, Sensory Transduction, Transducer, Vision, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Shimamura, K. Hiraki, N. Takahashi, T. Hori, H. Ago, K. Masuda, K. Takio, M. Ishiguro, M. Miyano
Crystal Structure Of Squid Rhodopsin With Intracellularly Extended Cytoplasmic Region
J. Biol. Chem. V. 283 17753 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 3)
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All Hetero Components
1a: PALMITIC ACID (PLMa)
1b: PALMITIC ACID (PLMb)
2a: RETINAL (RETa)
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No.
Name
Count
Type
Full Name
1
PLM
2
Ligand/Ion
PALMITIC ACID
2
RET
1
Ligand/Ion
RETINAL
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Sites
(3, 3)
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:120 , CYS A:186 , MET A:204 , PHE A:209 , TRP A:274 , LYS A:305
BINDING SITE FOR RESIDUE RET A 380
2
AC2
SOFTWARE
CYS A:336
BINDING SITE FOR RESIDUE PLM A 381
3
AC3
SOFTWARE
SER A:316 , CYS A:336 , CYS A:337
BINDING SITE FOR RESIDUE PLM A 382
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
(2, 2)
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1: G_PROTEIN_RECEP_F1_1 (A:121-137)
2: OPSIN (A:299-315)
;
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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_TODPA
121-137
1
A:121-137
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_TODPA
299-315
1
A:299-315
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Exons
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SCOP Domains
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CATH Domains
(1, 1)
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all CATH domains
1a: CATH_2ziyA01 (A:10-360)
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Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Todarodes pacificus. Japanese flying squid
(2)
1a
2ziyA01
A:10-360
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Asymmetric Unit 1
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