2Z73 - JenaLib

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Biological Unit 4 (Jmol Viewer)

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
PubMed-ID: 18480818 | Reference-DOI: 10.1038/NATURE06925
(for further references see the PDB file header)

Molecule 1 - RHODOPSIN
	Chains	:	A, B
	Organism Common	:	JAPANESE FLYING SQUID
	Organism Scientific	:	TODARODES PACIFICUS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A
Biological Unit 4 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 12)

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

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PC1	-1	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3	PLM	2	Ligand/Ion	PALMITIC ACID
4	RET	1	Ligand/Ion	RETINAL
5	SO4	-1	Ligand/Ion	SULFATE ION
6	TWT	1	Ligand/Ion	DOCOSANE

Biological Unit 2 (6, 7)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PC1	1	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3	PLM	2	Ligand/Ion	PALMITIC ACID
4	RET	1	Ligand/Ion	RETINAL
5	SO4	1	Ligand/Ion	SULFATE ION
6	TWT	1	Ligand/Ion	DOCOSANE

Biological Unit 3 (4, 5)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PC1	-1	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3	PLM	2	Ligand/Ion	PALMITIC ACID
4	RET	1	Ligand/Ion	RETINAL
5	SO4	-1	Ligand/Ion	SULFATE ION
6	TWT	1	Ligand/Ion	DOCOSANE

Biological Unit 4 (6, 14)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PC1	2	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3	PLM	4	Ligand/Ion	PALMITIC ACID
4	RET	2	Ligand/Ion	RETINAL
5	SO4	2	Ligand/Ion	SULFATE ION
6	TWT	2	Ligand/Ion	DOCOSANE

Asymmetric Unit (11, 11)

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

Asymmetric Unit

No.	Residues
1	A:108	-	A:186
2	B:108	-	B:186

Asymmetric Unit

No.	Residues
1	Phe A:89	-	Pro A:90
2	Phe B:89	-	Pro B:90

(no "SAP(SNP)/Variant" information available for 2Z73)

Asymmetric Unit (2, 4)

	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

Biological Unit 1 (2, 2)

	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 -

Biological Unit 2 (2, 2)

	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	- B:121-137
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_TODPA	299-315	1	- B:299-315

Biological Unit 3 (2, 2)

	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 -

Biological Unit 4 (2, 4)

	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	- B:121-137
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_TODPA	299-315	2	- B:299-315

(no "Exon" information available for 2Z73)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:350
 aligned with OPSD_TODPA | P31356 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:350
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
           OPSD_TODPA     9 ETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGE 358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2z73A01 A:10-358 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F-----------------------------------------------------------------------------------------------------------------------------------------------------------------OPSIN            ------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z73 A   9 ETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGE 358
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358

Chain B from PDB  Type:PROTEIN  Length:347
 aligned with OPSD_TODPA | P31356 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:347
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       
           OPSD_TODPA     9 ETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIP 355
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2z73B01 B:10-355 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ------------------------------------------7tm_1-2z73B01 B:51-315                                                                                                                                                                                                                                                   ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------7tm_1-2z73B02 B:51-315                                                                                                                                                                                                                                                   ---------------------------------------- Pfam domains (2)
         Sec.struct. author ...........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F-----------------------------------------------------------------------------------------------------------------------------------------------------------------OPSIN            ---------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z73 B   9 ETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIP 355
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2Z73)

Asymmetric Unit

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)

Todarodes pacificus. Japanese flying squid (2)

1a	2z73B01	B:10-355
1b	2z73A01	A:10-358

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (OPSD_TODPA | P31356)

molecular function
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	2z73
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	OPSD_TODPA \| P31356	:	2ziy 3aym 3ayn 4ww3

(no "Related Entries Specified in the PDB File" available for 2Z73)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (11, 11)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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