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2Z73
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (121 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SQUID RHODOPSIN
Authors
:
M. Murakami, T. Kouyama
Date
:
13 Aug 07 (Deposition) - 13 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A (1x)
Biol. Unit 4: B (2x)
Keywords
:
Visual Pigment, Gq-Type, G-Protein Coupled Receptor, Chromophore, Glycoprotein, Lipoprotein, Membrane, Palmitate, Phosphorylation, Photoreceptor Protein, Retinal Protein, Sensory Transduction, Transducer, Transmembrane, Vision, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Murakami, T. Kouyama
Crystal Structure Of Squid Rhodopsin.
Nature V. 453 363 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: B-OCTYLGLUCOSIDE (BOGa)
1b: B-OCTYLGLUCOSIDE (BOGb)
2a: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1a)
3a: PALMITIC ACID (PLMa)
3b: PALMITIC ACID (PLMb)
3c: PALMITIC ACID (PLMc)
3d: PALMITIC ACID (PLMd)
4a: RETINAL (RETa)
4b: RETINAL (RETb)
5a: SULFATE ION (SO4a)
6a: DOCOSANE (TWTa)
6b: DOCOSANE (TWTb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
2
PC1
1
Ligand/Ion
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3
PLM
4
Ligand/Ion
PALMITIC ACID
4
RET
2
Ligand/Ion
RETINAL
5
SO4
1
Ligand/Ion
SULFATE ION
6
TWT
2
Ligand/Ion
DOCOSANE
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:67 , ALA A:69 , ASN A:70 , ILE A:73 , ARG A:133 , LYS A:146 , GLU A:256 , LEU A:259 , SER A:263 , LYS A:321 , ASP A:347 , GLU A:351
BINDING SITE FOR RESIDUE BOG A 1005
02
AC2
SOFTWARE
THR B:67 , ASN B:70 , ILE B:73 , GLU B:256 , LEU B:259 , ILE B:262 , ASP B:347 , GLU B:351
BINDING SITE FOR RESIDUE BOG B 1005
03
AC3
SOFTWARE
ARG B:139 , SER B:148 , ARG B:150 , ARG B:151
BINDING SITE FOR RESIDUE SO4 B 1006
04
AC4
SOFTWARE
GLY A:112 , GLY A:116 , PHE A:120 , CYS A:186 , SER A:187 , PHE A:188 , PHE A:209 , TRP A:274 , ALA A:278 , LYS A:305
BINDING SITE FOR RESIDUE RET A 1000
05
AC5
SOFTWARE
LYS A:61 , PHE A:78 , SER B:16 , PHE B:103
BINDING SITE FOR RESIDUE PLM A 1001
06
AC6
SOFTWARE
MET A:313 , SER A:316 , CYS A:337
BINDING SITE FOR RESIDUE PLM A 1002
07
AC7
SOFTWARE
GLY A:51 , PRO A:312 , PHE B:97
BINDING SITE FOR RESIDUE TWT A 1003
08
AC8
SOFTWARE
ASN B:87 , GLY B:112 , GLY B:116 , PHE B:120 , CYS B:186 , TRP B:274 , ALA B:278 , LYS B:305
BINDING SITE FOR RESIDUE RET B 1000
09
AC9
SOFTWARE
SER A:16 , PHE A:103 , GLY A:104 , LYS B:61 , PHE B:78 , PHE B:81
BINDING SITE FOR RESIDUE PLM B 1001
10
BC1
SOFTWARE
MET B:313 , SER B:316 , CYS B:337
BINDING SITE FOR RESIDUE PLM B 1002
11
BC2
SOFTWARE
LEU B:161 , ARG B:193 , SER B:195 , ARG B:198 , SER B:199
BINDING SITE FOR RESIDUE PC1 B 1004
[
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:121-137,B:121-137)
2: OPSIN (A:299-315,B:299-315)
;
View:
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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_TODPA
121-137
2
A:121-137
B:121-137
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_TODPA
299-315
2
A:299-315
B:299-315
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2z73B01 (B:10-355)
1b: CATH_2z73A01 (A:10-358)
View:
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Classes
(
)
(
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)
(
)
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)
Todarodes pacificus. Japanese flying squid
(2)
1a
2z73B01
B:10-355
1b
2z73A01
A:10-358
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_7tm_1_2z73B01 (B:51-315)
1b: PFAM_7tm_1_2z73B02 (B:51-315)
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)
Clan
:
GPCR_A
(90)
Family
:
7tm_1
(47)
Todarodes pacificus (Japanese flying squid) (Ommastrephes pacificus)
(1)
1a
7tm_1-2z73B01
B:51-315
1b
7tm_1-2z73B02
B:51-315
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Asymmetric Unit 1
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Asym.Unit (127 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 KB)
Header - Biol.Unit 2
Biol.Unit 3 (61 KB)
Header - Biol.Unit 3
Biol.Unit 4 (121 KB)
Header - Biol.Unit 4
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