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(-) Description

Title :  STRUCTURE OF BACTERIORHODOPSIN AT 100 K
 
Authors :  K. Takeda, Y. Matsui, H. Sato, T. Hino, E. Kanamori, H. Okumura, T. Yamane, N. Kamiya, T. Kouyama
Date :  22 Sep 99  (Deposition) - 16 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Bacteriorhodopsin, Proton Pump, Membrane Protein, Retinal Protein, Photoreceptor, Lipid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Takeda, H. Sato, T. Hino, M. Kono, K. Fukuda, I. Sakurai, T. Okada, T. Kouyama
A Novel Three-Dimensional Crystal Of Bacteriorhodopsin Obtained By Successive Fusion Of The Vesicular Assemblies.
J. Mol. Biol. V. 283 463 1998
PubMed-ID: 9769218  |  Reference-DOI: 10.1006/JMBI.1998.2103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Cellular Location: CELL MEMBRANE
    Chains: A
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Other Details: 5 LIPIDS AND 23 WATER MOLECULES
    Strain: JW3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 9)

Asymmetric Unit (8, 9)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3L1P1Ligand/Ion3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
4L2P2Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
5L3P1Ligand/Ion2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
6L4P1Ligand/Ion3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
7MAN1Ligand/IonALPHA-D-MANNOSE
8RET1Ligand/IonRETINAL
Biological Unit 1 (8, 27)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2GLC3Ligand/IonALPHA-D-GLUCOSE
3L1P3Ligand/Ion3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
4L2P6Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
5L3P3Ligand/Ion2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
6L4P3Ligand/Ion3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
7MAN3Ligand/IonALPHA-D-MANNOSE
8RET3Ligand/IonRETINAL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:67 , LEU A:127 , L2P A:270 , MAN A:410BINDING SITE FOR RESIDUE GLC A 400
2AC2SOFTWARETYR A:64 , LEU A:66 , THR A:67 , TRP A:80 , LYS A:129 , L2P A:270 , GLC A:400 , GAL A:420 , HOH A:2014BINDING SITE FOR RESIDUE MAN A 410
3AC3SOFTWAREMAN A:410BINDING SITE FOR RESIDUE GAL A 420
4AC4SOFTWARETRP A:86 , THR A:89 , THR A:90 , MET A:118 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , ALA A:215 , LYS A:216BINDING SITE FOR RESIDUE RET A 250
5AC5SOFTWARELEU A:28 , LYS A:40 , ALA A:44 , ALA A:51 , PHE A:54 , THR A:107 , ALA A:110 , ILE A:117 , ILE A:140 , ALA A:144 , LEU A:146 , TYR A:147 , TYR A:150 , L3P A:280 , L2P A:300 , HOH A:2020 , HOH A:2021BINDING SITE FOR RESIDUE L1P A 260
6AC6SOFTWARETYR A:64 , TRP A:80 , ALA A:84 , PHE A:88 , LEU A:109 , GLY A:113 , ILE A:117 , GLY A:120 , LEU A:123 , VAL A:124 , LEU A:127 , GLC A:400 , MAN A:410BINDING SITE FOR RESIDUE L2P A 270
7AC7SOFTWAREGLY A:6 , ALA A:14 , ALA A:18 , MET A:60 , LEU A:61 , LEU A:62 , GLY A:63 , TYR A:133 , L1P A:260 , HOH A:2022 , HOH A:2023BINDING SITE FOR RESIDUE L3P A 280
8AC8SOFTWARELEU A:22 , TYR A:131 , SER A:132 , PHE A:135 , ALA A:139 , ALA A:196BINDING SITE FOR RESIDUE L4P A 290
9AC9SOFTWARELEU A:19 , TYR A:26 , TYR A:150 , LEU A:221 , ARG A:225 , L1P A:260BINDING SITE FOR RESIDUE L2P A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QM8)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107  1A:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232  1A:208-219
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107  3A:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232  3A:208-219

(-) Exons   (0, 0)

(no "Exon" information available for 1QM8)

(-) 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:229
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:229
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234         
           BACR_HALSA    15 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 243
               SCOP domains d1qm8a_ A: Bacteriorhodopsin                                                                                                                                                                                                          SCOP domains
               CATH domains 1qm8A00 A:2-230 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qm8 A   2 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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 '|'

 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 1QM8)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (BACR_HALSA | P02945)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BACR_HALSA | P02945: 1ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1ixf 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1r2n 1r84 1s51 1s52 1s53 1s54 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4md2 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9

(-) Related Entries Specified in the PDB File

1ap9 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES
1at9 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY
1bac RHODOPSIN (7-HELIX BUNDLE) COMPLEX WITH ALL-TRANS RETINAL (THEORETICAL MODEL)
1bad BACTERIORHODOPSIN (7-HELIX BUNDLE) WITH 13-CIS RETINAL (THEORETICAL MODEL)
1bct BACTERIORHODOPSIN (FRAGMENT 163-231) (NMR, 14 STRUCTURES)
1bha BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71, SOLUBILIZED IN SDS MICELLES) (NMR, 12 STRUCTURES)
1bhb BACTERIORHODOPSIN (PROTEOLYTIC FRAGMENT 1 - 71, SOLUBILIZED IN METHANOL-CHLOROFORM) (NMR, 12 STRUCTURES)
1brd BACTERIORHODOPSIN, HALOBACTERIUM HALOBIUM, ELECTRON DIFFRACTION
1brr X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX
1c3w BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION (GROUND STATE WILD TYPE "BR")
2brd CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE