2JAG - JenaLib

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Title :   L1-INTERMEDIATE OF HALORHODOPSIN T203V

Authors :   W. Gmelin, K. Zeth, R. Efremov, J. Heberle, J. Tittor, D. Oesterhelt

Date :   28 Nov 06 (Deposition) - 14 Dec 06 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Chromophore, Chloride Pump, Ion Transport, Membrane Protein, Sensory Transduction, Membrane, Chloride, Receptor, Ion Pump, Transport, Photoreceptor Protein, Transmembrane, Retinal Protein, Intermediate L1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Gmelin, K. Zeth, R. Efremov, J. Heberle, J. Tittor, D. Oesterhelt
The Crystal Structure Of The L1 Intermediate Of Halorhodopsin At 1. 9 Angstroms Resolution.
Photochem. Photobiol. V. 83 369 2007
PubMed-ID: 17117890 | Reference-DOI: 10.1562/2006-06-23-RA-947

Molecule 1 - HALORHODOPSIN
	Chains	:	A
	Mutation	:	YES
	Organism Scientific	:	HALOBACTERIUM SALINARIUM
	Organism Taxid	:	2242
	Other Details	:	DSM 671
	Strain	:	R1
	Synonym	:	HR

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	PLM	1	Ligand/Ion	PALMITIC ACID
4	RET	1	Ligand/Ion	RETINAL

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PLM	3	Ligand/Ion	PALMITIC ACID
4	RET	3	Ligand/Ion	RETINAL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:94 , HIS A:95 , ALA A:96 , TRP A:162 , VAL A:180 , THR A:181 , GLY A:220 , LEU A:221	BINDING SITE FOR RESIDUE BOG A 801
2	AC2	SOFTWARE	THR A:111 , TRP A:112 , SER A:115 , LYS A:242 , HOH A:2019 , HOH A:2020	BINDING SITE FOR RESIDUE CL A 501
3	AC3	SOFTWARE	ARG A:24 , LEU A:29 , ARG A:103 , GLN A:105	BINDING SITE FOR RESIDUE CL A 502
4	AC4	SOFTWARE	SER A:75 , SER A:76 , THR A:111 , MET A:118 , PHE A:135 , ALA A:139	BINDING SITE FOR RESIDUE PLM A 700
5	AC5	SOFTWARE	TRP A:112 , SER A:115 , THR A:116 , TYR A:165 , SER A:168 , TRP A:207 , TYR A:210 , PRO A:211 , ASP A:238 , ALA A:241 , LYS A:242	BINDING SITE FOR RESIDUE RET A 900

(no "SS Bond" information available for 2JAG)

(no "Cis Peptide Bond" information available for 2JAG)

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACH_HALS3	108-120	1	A:108-120
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACH_HALSA	108-120	1	A:108-120
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACH_HALS3	234-245	1	A:234-245
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACH_HALSA	234-245	1	A:234-245

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACH_HALS3	108-120	3	A:108-120
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACH_HALSA	108-120	3	A:108-120
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACH_HALS3	234-245	3	A:234-245
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACH_HALSA	234-245	3	A:234-245

(no "Exon" information available for 2JAG)

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
	(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:242
 aligned with BACH_HALS3 | B0R2U4 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:242
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
           BACH_HALS3    22 AVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVFAKYVFAFILLRWVANNERTVAVA 263
               SCOP domains d2jaga_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jagA00 A:22-263 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........eeeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE (1)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jag A  22 AVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLVVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNERTVAVA 263
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain A from PDB  Type:PROTEIN  Length:242
 aligned with BACH_HALSA | P0DMH7 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:242
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
           BACH_HALSA    22 AVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVFAKYVFAFILLRWVANNERTVAVA 263
               SCOP domains d2jaga_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jagA00 A:22-263 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........eeeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jag A  22 AVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLVVVLWLGYPIVWAVGVEGLALVQSVGATSWAYSVLDVFAKYVFAFILLRWVANNERTVAVA 263
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 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: automated matches (33)

Halobacterium salinarium [TaxId: 2242] (3)

d2jaga_

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)

Halobacterium salinarium. Organism_taxid: 2242. Strain: r1. (2)

2jagA00

A:22-263

(no "Pfam Domain" information available for 2JAG)

Asymmetric Unit(hide GO term definitions)

Chain A (BACH_HALS3 | B0R2U4)

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.

Chain A (BACH_HALSA | P0DMH7)

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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jag)

Biological Unit
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	BACH_HALSA \| P0DMH7
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UniProtKB/Swiss-Prot
	BACH_HALS3 \| B0R2U4	:	1e12 2jaf 5ahy 5ahz 5g36
	BACH_HALSA \| P0DMH7	:	1e12 2jaf

1e12	HALORHODOPSIN, A LIGHT-DRIVEN CHLORIDE PUMP
2jaf	GROUND STATE AND L1 INTERMEDIATE OF HALORHODOPSIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (2, 2)

Exons (0, 0)

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CATH Domains (1, 1)

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Gene Ontology (11, 22)

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