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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-1

Authors :   N. Enami, H. Okumua, T. Kouyama

Date :   26 Mar 03 (Deposition) - 15 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

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

Keywords :   Proton Pump, Retinal Protein, 7 Trans-Membrane Helices, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Enami, H. Okumua, T. Kouyama
X-Ray Crystallographic Studies Of Archaerhodopsin
J. Photosci. V. 9 320 2003
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ARCHAERHODOPSIN-1
	Chains	:	A, B
	Organism Scientific	:	HALOBACTERIUM SP. AUS-1
	Organism Taxid	:	2244
	Strain	:	AUS-1
	Synonym	:	AR 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	RET	2	Ligand/Ion	RETINAL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:92 , THR A:96 , TRP A:144 , SER A:147 , THR A:148 , TRP A:188 , TYR A:191 , PRO A:192 , TRP A:195 , ASP A:218 , ALA A:221 , LYS A:222	BINDING SITE FOR RESIDUE RET A 255
2	AC2	SOFTWARE	TRP B:92 , THR B:96 , MET B:124 , TRP B:144 , SER B:147 , THR B:148 , MET B:151 , TRP B:188 , TYR B:191 , PRO B:192 , TRP B:195 , ASP B:218 , LYS B:222	BINDING SITE FOR RESIDUE RET B 255

(no "SS Bond" information available for 1UAZ)

(no "Cis Peptide Bond" information available for 1UAZ)

(no "SAP(SNP)/Variant" information available for 1UAZ)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACR1_HALC1	94-106	2	A:88-100 B:88-100
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACR1_HALSS	94-106	2	A:88-100 B:88-100
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR1_HALC1	220-231	2	A:214-225 B:214-225
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR1_HALSS	220-231	2	A:214-225 B:214-225

(no "Exon" information available for 1UAZ)

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:236
 aligned with BACR1_HALC1 | P69051 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:236
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236      
          BACR1_HALC1     7 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 242
               SCOP domains d1uaza_ A: Archaerhodopsin-1                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uazA00 A:1-236 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaz A   1 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain A from PDB  Type:PROTEIN  Length:236
 aligned with BACR1_HALSS | P69052 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:236
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236      
          BACR1_HALSS     7 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 242
               SCOP domains d1uaza_ A: Archaerhodopsin-1                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uazA00 A:1-236 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaz A   1 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with BACR1_HALC1 | P69051 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:236
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236      
          BACR1_HALC1     7 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 242
               SCOP domains d1uazb_ B: Archaerhodopsin-1                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uazB00 B:1-236 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaz B   1 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with BACR1_HALSS | P69052 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:236
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236      
          BACR1_HALSS     7 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 242
               SCOP domains d1uazb_ B: Archaerhodopsin-1                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uazB00 B:1-236 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaz B   1 TAAVGADLLGDGRPETLWLGIGTLLMLIGTFYFIVKGWGVTDKEAREYYSITILVPGIASAAYLSMFFGIGLTEVQVGSEMLDIYYARYADWLFTTPLLLLDLALLAKVDRVSIGTLVGVDALMIVTGLVGALSHTPLARYTWWLFSTICMIVVLYFLATSLRAAAKERGPEVASTFNTLTALVLVLWTAYPILWIIGTEGAGVVGLGIETLLFMVLDVTAKVGFGFILLRSRAIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: Bacteriorhodopsin-like (107)

Protein domain: Archaerhodopsin-1 (1)

Halobacterium sp. [TaxId: 2243] (1)

1a	d1uaza_	A:
1b	d1uazb_	B:

Asymmetric/Biological 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)

Aus-1 (Halobacterium sp) (1)

1a	1uazA00	A:1-236
1b	1uazB00	B:1-236

(no "Pfam Domain" information available for 1UAZ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BACR1_HALC1 | P69051)

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:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.

Chain A,B (BACR1_HALSS | P69052)

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:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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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1iw6	BACTERIORHODOPSIN IN THE P622 CRYSTAL

Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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