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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ANION-FREE BLUE FORM OF PHARAONIS HALORHODOPSIN

Authors :   T. Kouyama, S. Kanada

Date :   13 Jan 11 (Deposition) - 31 Aug 11 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   S. Kanada, Y. Takeguchi, M. Murakami, K. Ihara, T. Kouyama
Crystal Structures Of An O-Like Blue Form And An Anion-Free Yellow Form Of Pharaonis Halorhodopsin
J. Mol. Biol. V. 413 162 2011
PubMed-ID: 21871461 | Reference-DOI: 10.1016/J.JMB.2011.08.021

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, 9)

No.	Name	Count	Type	Full Name
1	22B	2	Ligand/Ion	BACTERIORUBERIN
2	BNG	4	Ligand/Ion	B-NONYLGLUCOSIDE
3	RET	3	Ligand/Ion	RETINAL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:127 , SER A:130 , THR A:131 , MET A:159 , TYR A:180 , SER A:183 , TRP A:222 , TYR A:225 , TRP A:229 , ASP A:252 , LYS A:256	BINDING SITE FOR RESIDUE RET A 292
2	AC2	SOFTWARE	ALA A:98 , GLY A:99 , HIS A:173 , LEU A:174 , TRP A:177 , HOH A:521 , HOH A:533 , ASP B:209 , BNG B:402 , HOH B:571	BINDING SITE FOR RESIDUE BNG A 403
3	AC3	SOFTWARE	GLY A:99 , PHE A:101 , HOH A:533 , ASP B:209	BINDING SITE FOR RESIDUE BNG A 404
4	AC4	SOFTWARE	PHE A:25 , GLU A:26 , HOH D:612	BINDING SITE FOR RESIDUE BNG A 405
5	AC5	SOFTWARE	TRP B:127 , SER B:130 , THR B:131 , MET B:159 , GLY B:163 , TYR B:180 , SER B:183 , PHE B:187 , TRP B:222 , TYR B:225 , PRO B:226 , ASP B:252 , LYS B:256	BINDING SITE FOR RESIDUE RET B 292
6	AC6	SOFTWARE	PHE A:155 , ILE A:193 , GLU A:197 , ILE B:49 , VAL B:53 , THR B:56 , VAL B:69 , ILE B:72 , HOH B:575 , HOH B:576	BINDING SITE FOR RESIDUE 22B B 300
7	AC7	SOFTWARE	BNG A:403 , HOH A:521 , HOH A:536 , HOH A:578 , PHE B:25 , GLU B:26 , SER B:269 , ASN B:270 , HOH B:517 , HOH B:535 , HOH B:571	BINDING SITE FOR RESIDUE BNG B 402
8	AC8	SOFTWARE	TRP D:127 , SER D:130 , THR D:131 , MET D:159 , TYR D:180 , 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
9	AC9	SOFTWARE	ILE A:49 , VAL A:53 , LYS A:65 , ILE A:72 , ILE A:79 , PHE D:155 , VAL D:189 , TYR D:192 , GLU D:197 , HOH D:565 , HOH D:572	BINDING SITE FOR RESIDUE 22B D 300

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

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

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

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 3QBG)

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:261
 aligned with BACH_NATPH | P15647 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:261
                                    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 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFLVVLYILLVEWAQDAKAAGTADMFNTLKLLTVVMWLGYPIVWALGVEGIAVLPVGVTSWGYSFLDIVAKYIFAFLLLNYLTSNESVVSGSI 278
               SCOP domains d3qbga_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbg A  18 EVTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGSI 278
                                    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: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 d3qbgb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbg B  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 D 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 d3qbgd_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee...........eeee..eeee.eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbg D  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

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	d3qbga_	A:
1b	d3qbgb_	B:
1c	d3qbgd_	D:

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

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

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 3qbg)

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

3a7k	THE CHLORIDE-BOUND FORM OF PHARAONIS HALORHODOPSIN
3qbi	ANION-FREE YELLOW FORM OF PHARAONIS HALORHODOPSIN
3qbk	BROMIDE-BOUND FORM OF PHARAONIS HALORHODOPSIN
3qbl	PHARAONIS HALORHODOPSIN COMPLEXED WITH NITRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

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

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 16)

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