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1GZM
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (119 KB)
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(1)
Title
:
STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM
Authors
:
J. Li
Date
:
24 May 02 (Deposition) - 20 Nov 03 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Signaling Protein, Photoreceptor, Retinal Protein, Visual Pigment, G-Protein Coupled Receptor, Integral Membrane Protein, Palmitate, Phosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Li, P. Edwards, M. Burghammer, C. Villa, G. F. X. Schertler
Structure Of Bovine Rhodopsin In A Trigonal Crystal Form
J. Mol. Biol. V. 343 1409 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 39)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
3a: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ea)
3b: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eb)
3c: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ec)
3d: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ed)
3e: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ee)
3f: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ef)
3g: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eg)
3h: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eh)
3i: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ei)
3j: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ej)
3k: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ek)
3l: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8El)
4a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
4b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
4c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6a: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHA... (PEFa)
6b: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHA... (PEFb)
7a: PALMITIC ACID (PLMa)
7b: PALMITIC ACID (PLMb)
7c: PALMITIC ACID (PLMc)
7d: PALMITIC ACID (PLMd)
8a: RETINAL (RETa)
8b: RETINAL (RETb)
9a: ZINC ION (ZNa)
9b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
2
Mod. Amino Acid
ACETYL GROUP
2
BMA
4
Ligand/Ion
BETA-D-MANNOSE
3
C8E
12
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
4
LDA
3
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PEF
2
Ligand/Ion
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
7
PLM
4
Ligand/Ion
PALMITIC ACID
8
RET
2
Ligand/Ion
RETINAL
9
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:147 , GLY A:149 , ASN A:151 , HIS A:152
BINDING SITE FOR RESIDUE ZN A1349
02
AC2
SOFTWARE
ALA A:117 , THR A:118 , GLY A:121 , GLU A:122 , CYS A:187 , ILE A:189 , TYR A:191 , MET A:207 , PHE A:212 , PHE A:261 , TRP A:265 , TYR A:268 , ALA A:292 , LYS A:296
BINDING SITE FOR RESIDUE RET A1332
03
AC3
SOFTWARE
LEU A:50 , ILE A:54 , MET A:163 , VAL A:210 , LEU A:321 , CYS A:322
BINDING SITE FOR RESIDUE PLM A1333
04
AC4
SOFTWARE
PHE A:52 , PHE A:56 , TYR A:60 , LEU A:321 , CYS A:322 , CYS A:323
BINDING SITE FOR RESIDUE PLM A1334
05
AC5
SOFTWARE
ALA A:260 , THR A:297
BINDING SITE FOR RESIDUE PEF A1341
06
AC6
SOFTWARE
LEU A:266 , GLY A:270 , PHE A:273
BINDING SITE FOR RESIDUE LDA A1342
07
AC7
SOFTWARE
TYR A:43 , PRO A:267 , ILE A:290 , PRO A:291 , PHE A:294
BINDING SITE FOR RESIDUE C8E A1343
08
AC8
SOFTWARE
THR A:108 , ASN A:111 , HOH A:2005
BINDING SITE FOR RESIDUE C8E A1344
09
AC9
SOFTWARE
ILE A:259 , THR B:277 , C8E B:1340
BINDING SITE FOR RESIDUE C8E A1345
10
BC1
SOFTWARE
ASN A:199 , ARG A:314 , ASN A:315
BINDING SITE FOR RESIDUE C8E A1346
11
BC2
SOFTWARE
PHE A:273 , TYR A:274 , LEU B:262
BINDING SITE FOR RESIDUE C8E A1347
12
BC3
SOFTWARE
PHE A:221 , VAL B:209
BINDING SITE FOR RESIDUE C8E A1348
13
BC4
SOFTWARE
ALA B:117 , THR B:118 , GLY B:121 , GLU B:122 , CYS B:187 , ILE B:189 , TYR B:191 , MET B:207 , PHE B:212 , PHE B:261 , TRP B:265 , TYR B:268 , ALA B:292 , LYS B:296
BINDING SITE FOR RESIDUE RET B1332
14
BC5
SOFTWARE
PRO B:53 , ILE B:54 , VAL B:162 , MET B:163 , VAL B:210 , LEU B:321 , CYS B:322
BINDING SITE FOR RESIDUE PLM B1333
15
BC6
SOFTWARE
PHE B:52 , PHE B:159 , VAL B:162 , MET B:163 , LEU B:321 , CYS B:322 , CYS B:323
BINDING SITE FOR RESIDUE PLM B1334
16
BC7
SOFTWARE
ACE A:0 , ASN A:2 , GLY A:280 , ASP A:282
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 2 RESIDUES 1338 TO 1340
17
BC8
SOFTWARE
THR A:4 , ASN A:15 , GLY A:18 , VAL A:20 , ARG A:21
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 15 RESIDUES 1335 TO 1337
18
BC9
SOFTWARE
ACE B:0 , MET B:1 , ASN B:2 , ASP B:282
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 2 RESIDUES 1337 TO 1339
19
CC1
SOFTWARE
ILE A:259 , LEU A:262 , THR A:277 , C8E A:1345 , ACE B:0 , MET B:1 , ASN B:2 , THR B:4 , ASN B:15 , GLY B:18 , VAL B:20 , TYR B:43 , THR B:108 , ASN B:111 , ARG B:147 , GLY B:149 , ASN B:151 , HIS B:152 , ASN B:199 , PHE B:208 , ILE B:259 , LEU B:266 , PRO B:267 , GLY B:270 , VAL B:271 , PHE B:273 , TYR B:274 , THR B:277 , ASP B:282 , PHE B:287 , ILE B:290 , PRO B:291 , PHE B:294 , THR B:297 , ILE B:305 , ARG B:314 , HOH B:2006
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 15 RESIDUES 1335 TO 1350
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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)
Exon 1.3 (A:180-235 | B:180-235)
Exon 1.4 (A:236-315 | B:236-315)
Exon 1.5 (A:316-332 (gaps) | B:316-332 (gaps...)
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
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:316-332 (gaps)
B:316-332 (gaps)
17
17
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1gzma_ (A:)
1b: SCOP_d1gzmb_ (B:)
View:
Select:
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
d1gzma_
A:
1b
d1gzmb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1gzmA00 (A:1-332)
1b: CATH_1gzmB00 (B:1-332)
View:
Select:
Label:
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)
Bovine (Bos taurus)
(4)
1a
1gzmA00
A:1-332
1b
1gzmB00
B:1-332
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
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Asymmetric Unit 1
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