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(-) Description

Title :  GROUND STATE 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 :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Chromophore, Chloride Pump, Ion Transport, Membrane, Chloride, Receptor, Ion Pump, Transport, Sensory Transduction, Photoreceptor Protein, Transmembrane, Retinal Protein, Membrane Protein (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

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE
2CL2Ligand/IonCHLORIDE ION
3PLM2Ligand/IonPALMITIC ACID
4RET1Ligand/IonRETINAL
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1BOG3Ligand/IonB-OCTYLGLUCOSIDE
2CL-1Ligand/IonCHLORIDE ION
3PLM6Ligand/IonPALMITIC ACID
4RET3Ligand/IonRETINAL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:94 , HIS A:95 , ALA A:96 , LEU A:158 , TRP A:162 , VAL A:180 , GLY A:220 , LEU A:221BINDING SITE FOR RESIDUE BOG A 801
2AC2SOFTWARETHR A:111 , SER A:115 , LYS A:242 , HOH A:2026BINDING SITE FOR RESIDUE CL A 501
3AC3SOFTWAREARG A:24 , ARG A:103 , GLN A:105BINDING SITE FOR RESIDUE CL A 502
4AC4SOFTWARESER A:75 , SER A:76 , LEU A:110 , THR A:111 , ALA A:113 , PHE A:135 , VAL A:146 , PHE A:164BINDING SITE FOR RESIDUE PLM A 700
5AC5SOFTWARETRP A:106 , MET A:153BINDING SITE FOR RESIDUE PLM A 701
6AC6SOFTWARETRP A:112 , THR A:116 , MET A:144 , TYR A:165 , SER A:168 , TRP A:207 , TYR A:210 , PRO A:211 , ASP A:238 , LYS A:242BINDING SITE FOR RESIDUE RET A 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACH_HALS3108-120  1A:108-120
BACH_HALSA108-120  1A:108-120
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACH_HALS3234-245  1A:234-245
BACH_HALSA234-245  1A:234-245
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACH_HALS3108-120  3A:108-120
BACH_HALSA108-120  3A:108-120
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACH_HALS3234-245  3A:234-245
BACH_HALSA234-245  3A:234-245

(-) Exons   (0, 0)

(no "Exon" information available for 2JAF)

(-) Sequences/Alignments

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 d2jafa_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jafA00 A:22-263 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jaf 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 d2jafa_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jafA00 A:22-263 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jaf 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)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 22)

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.

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  2jaf
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  BACH_HALSA | P0DMH7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BACH_HALS3 | B0R2U4: 1e12 2jag 5ahy 5ahz 5g36
        BACH_HALSA | P0DMH7: 1e12 2jag

(-) Related Entries Specified in the PDB File

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