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Asym./Biol. Unit (Jmol Viewer)

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Title :   PHARAONIS HALORHODOPSIN COMPLEXED WITH NITRATE

Authors :   T. Kouyama, S. Kanada

Date :   13 Jan 11 (Deposition) - 31 Aug 11 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,D

Keywords :   Membrane Protein, Retinal Protein, Ion Pump (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kanada, Y. Takeguchi, M. Murakami, K. Ihara, T. Kouyama
Crystal Structures Of Anion-Free Blue And Yellow Forms Of Pharaonis Halorhodopsin
To Be Published
PubMed: search

Molecule 1 - HALORHODOPSIN
	Chains	:	A, B, D
	Organism Scientific	:	NATRONOMONAS PHARAONIS
	Organism Taxid	:	2257
	Other Details	:	STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T.
	Strain	:	MK-1

		1	2	3
Asymmetric/Biological Unit	:	A	B	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	22B	2	Ligand/Ion	BACTERIORUBERIN
2	NO3	6	Ligand/Ion	NITRATE ION
3	RET	3	Ligand/Ion	RETINAL

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:127 , THR A:131 , GLY A:163 , TYR A:180 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , ASP A:252 , LYS A:256	BINDING SITE FOR RESIDUE RET A 292
02	AC2	SOFTWARE	VAL A:77 , SER A:78 , SER A:81 , THR A:126 , TRP A:127 , SER A:130 , LYS A:256 , HOH A:502	BINDING SITE FOR RESIDUE NO3 A 359
03	AC3	SOFTWARE	ASN A:145 , THR A:147 , LYS A:148 , PRO B:62 , LYS B:65 , 22B B:300 , HOH B:527 , HOH B:531	BINDING SITE FOR RESIDUE NO3 A 360
04	AC4	SOFTWARE	PRO A:62 , LYS A:65 , ASN D:145 , THR D:147 , LYS D:148	BINDING SITE FOR RESIDUE NO3 A 293
05	AC5	SOFTWARE	TRP B:127 , THR B:131 , TYR B:180 , SER B:183 , TRP B:222 , TYR B:225 , PRO B:226 , ASP B:252 , LYS B:256	BINDING SITE FOR RESIDUE RET B 292
06	AC6	SOFTWARE	THR A:151 , PHE A:155 , VAL A:189 , ILE A:193 , NO3 A:360 , ILE B:49 , THR B:56 , ILE B:72	BINDING SITE FOR RESIDUE 22B B 300
07	AC7	SOFTWARE	VAL B:77 , SER B:78 , SER B:81 , THR B:126 , TRP B:127 , SER B:130 , LYS B:256 , HOH B:502 , HOH B:504	BINDING SITE FOR RESIDUE NO3 B 359
08	AC8	SOFTWARE	MET D:159 , SER D:183 , PHE D:187 , TRP D:222 , TYR D:225 , PRO D:226 , ASP D:252 , LYS D:256	BINDING SITE FOR RESIDUE RET D 292
09	AC9	SOFTWARE	ILE A:49 , THR A:56 , ILE A:72 , THR D:151 , PHE D:155 , ALA D:185 , VAL D:189 , ILE D:193 , GLU D:197	BINDING SITE FOR RESIDUE 22B D 300
10	BC1	SOFTWARE	ASN B:145 , THR B:147 , LYS B:148 , PRO D:62 , LYS D:65	BINDING SITE FOR RESIDUE NO3 D 360
11	BC2	SOFTWARE	VAL D:77 , SER D:78 , SER D:81 , THR D:126 , TRP D:127 , SER D:130 , LYS D:256 , HOH D:502 , HOH D:504	BINDING SITE FOR RESIDUE NO3 D 359

(no "SS Bond" information available for 3QBL)

(no "Cis Peptide Bond" information available for 3QBL)

(no "SAP(SNP)/Variant" information available for 3QBL)

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACH_NATPH	123-135	3	A:123-135 B:123-135 D:123-135
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACH_NATPH	248-259	3	A:248-259 B:248-259 D:248-259

(no "Exon" information available for 3QBL)

Asymmetric/Biological 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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:260
 aligned with BACH_NATPH | P15647 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:260
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
           BACH_NATPH    18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFLVVLYILLVEWAQDAKAAGTADMFNTLKLLTVVMWLGYPIVWALGVEGIAVLPVGVTSWGYSFLDIVAKYIFAFLLLNYLTSNESVVSGS 277
               SCOP domains d3qbla_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbl A  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGS 277
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with BACH_NATPH | P15647 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:259
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
           BACH_NATPH    18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFLVVLYILLVEWAQDAKAAGTADMFNTLKLLTVVMWLGYPIVWALGVEGIAVLPVGVTSWGYSFLDIVAKYIFAFLLLNYLTSNESVVSG 276
               SCOP domains d3qblb_ B: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbl B  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSG 276
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

Chain D from PDB  Type:PROTEIN  Length:259
 aligned with BACH_NATPH | P15647 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:259
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         
           BACH_NATPH    18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFLVVLYILLVEWAQDAKAAGTADMFNTLKLLTVVMWLGYPIVWALGVEGIAVLPVGVTSWGYSFLDIVAKYIFAFLLLNYLTSNESVVSG 276
               SCOP domains d3qbld_ D: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbl D  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSG 276
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

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 '\|'

Asymmetric/Biological Unit

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: automated matches (15)

Protein domain: automated matches (15)

Natronomonas pharaonis [TaxId: 2257] (5)

1a	d3qbla_	A:
1b	d3qblb_	B:
1c	d3qbld_	D:

(no "CATH Domain" information available for 3QBL)

(no "Pfam Domain" information available for 3QBL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,D (BACH_NATPH | P15647)

molecular function
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	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.
biological process
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qbl)

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UniProtKB/Swiss-Prot
	BACH_NATPH \| P15647	:	3qbg 3qbi 3qbk 3vvk

3a7k	CHLORIDE-BOUND FORM OF PHARAONIS HALORHDOPSIN
3qbg	ANION-FREE BLUE FORM OF PHARAONIS HALORHODOPSIN
3qbi	ANION-FREE YELLOW FORM OF PHARAONIS HALORHODOPSIN
3qbk	BROMIDE-BOUND FORM OF PHARAONIS HALORHODOPSIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 16)

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Related Entries Specified in the PDB File