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(-) Description

Title :  X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX
 
Authors :  L. -O. Essen, R. Siegert, D. Oesterhelt
Date :  28 Jul 98  (Deposition) - 30 Sep 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Proton Pump, Membrane Protein, Retinal Protein, Lipids, Photoreceptor, Haloarchaea, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Essen, R. Siegert, W. D. Lehmann, D. Oesterhelt
Lipid Patches In Membrane Protein Oligomers: Crystal Structure Of The Bacteriorhodopsin-Lipid Complex
Proc. Natl. Acad. Sci. Usa V. 95 11673 1998
PubMed-ID: 9751724  |  Reference-DOI: 10.1073/PNAS.95.20.11673
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (BACTERIORHODOPSIN)
    Cellular Location: MEMBRANE
    Chains: A, B, C
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Other Details: SCHIFF BASE BETWEEN LYS 216 AND RET 999
    Strain: R1
    Synonym: BR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 25)

Asymmetric/Biological Unit (9, 25)
No.NameCountTypeFull Name
1ARC10Ligand/Ion3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL
2BGC1Ligand/IonBETA-D-GLUCOSE
3GLC2Ligand/IonALPHA-D-GLUCOSE
4GOL3Ligand/IonGLYCEROL
5MAN2Ligand/IonALPHA-D-MANNOSE
6OCT1Ligand/IonN-OCTANE
7PCA1Mod. Amino AcidPYROGLUTAMIC ACID
8RET3Ligand/IonRETINAL
9SGA2Ligand/IonO3-SULFONYLGALACTOSE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARC A:1001 , GOL A:1003 , THR B:67 , LEU B:127 , MAN B:249 , ARC B:1002BINDING SITE FOR RESIDUE GLC B 248
02AC2SOFTWARETYR A:64 , LEU A:66 , THR A:67 , LYS B:129 , GLC B:248 , SGA B:250BINDING SITE FOR RESIDUE MAN B 249
03AC3SOFTWARELYS B:129 , MAN B:249BINDING SITE FOR RESIDUE SGA B 250
04AC4SOFTWARETHR A:67 , LEU A:127 , MAN C:249 , ARC C:1002 , GOL C:1003BINDING SITE FOR RESIDUE GLC C 248
05AC5SOFTWARETYR C:64 , LEU C:66 , THR C:67 , GLC C:248 , SGA C:250BINDING SITE FOR RESIDUE MAN C 249
06AC6SOFTWAREPRO A:70 , PHE A:71 , GLY A:72 , GLY A:73 , GLU A:74 , MAN C:249BINDING SITE FOR RESIDUE SGA C 250
07AC7SOFTWARELEU B:22 , OCT B:1004 , LEU C:22BINDING SITE FOR RESIDUE BGC B 251
08AC8SOFTWARETRP A:86 , THR A:89 , THR A:90 , MET A:118 , SER A:141 , THR A:142 , MET A:145 , TRP A:182 , TYR A:185 , PRO A:186 , ASP A:212 , LYS A:216BINDING SITE FOR RESIDUE RET A 999
09AC9SOFTWARETRP B:86 , THR B:89 , THR B:90 , MET B:118 , ILE B:119 , SER B:141 , THR B:142 , TRP B:182 , TYR B:185 , PRO B:186 , ASP B:212 , LYS B:216BINDING SITE FOR RESIDUE RET B 999
10BC1SOFTWARETRP C:86 , THR C:89 , THR C:90 , LEU C:93 , MET C:118 , SER C:141 , THR C:142 , MET C:145 , TRP C:182 , TYR C:185 , PRO C:186 , ASP C:212 , LYS C:216BINDING SITE FOR RESIDUE RET C 999
11BC2SOFTWAREALA B:184 , VAL B:187 , ALA C:184 , LEU C:207 , LEU C:211BINDING SITE FOR RESIDUE ARC C 1000
12BC3SOFTWARELEU B:28 , GLY B:31 , LYS B:40 , TYR B:43 , THR B:47 , LEU B:48 , GLY C:106 , THR C:107 , ALA C:110 , TYR C:147BINDING SITE FOR RESIDUE ARC C 1001
13BC4SOFTWAREGLY A:106 , THR A:107 , ALA A:110 , ALA A:114 , TYR A:147 , GLY C:31 , TYR C:43 , ALA C:44 , THR C:47 , LEU C:48BINDING SITE FOR RESIDUE ARC A 1000
14BC5SOFTWARELEU A:28 , TYR A:43 , ALA A:44 , THR A:47 , GLY B:106 , THR B:107 , ALA B:110 , ALA B:114 , ALA B:143 , ALA B:144 , TYR B:147BINDING SITE FOR RESIDUE ARC B 1000
15BC6SOFTWARETHR B:55 , TYR B:64 , PHE B:88 , LEU B:92 , ARC B:1002 , GOL B:1005 , GLY C:113 , GLY C:116 , VAL C:124BINDING SITE FOR RESIDUE ARC B 1001
16BC7SOFTWAREPHE B:88 , GLC B:248 , ARC B:1001 , GOL B:1005 , ARC C:1002BINDING SITE FOR RESIDUE ARC B 1002
17BC8SOFTWAREMET A:56 , TYR A:64 , TRP A:80 , PHE A:88 , ARC A:1001 , GOL A:1003 , GLY B:113 , GLY B:116 , GLY B:120BINDING SITE FOR RESIDUE ARC B 1003
18BC9SOFTWARETYR A:64 , TRP A:80 , LEU A:123 , GOL A:1003 , GLC B:248 , ARC B:1003 , ARC C:1002BINDING SITE FOR RESIDUE ARC A 1001
19CC1SOFTWAREVAL A:112 , GLY A:113 , ILE A:117 , GLY A:120 , VAL A:124 , THR C:55 , MET C:56 , TRP C:80 , PHE C:88 , ARC C:1002 , GOL C:1003BINDING SITE FOR RESIDUE ARC A 1002
20CC2SOFTWARELEU A:87 , ARC A:1001 , ARC A:1002 , ARC B:1002 , TRP C:80 , LEU C:87 , PHE C:88 , LEU C:123 , GLC C:248 , GOL C:1003BINDING SITE FOR RESIDUE ARC C 1002
21CC3SOFTWAREBGC B:251 , ILE C:11BINDING SITE FOR RESIDUE OCT B 1004
22CC4SOFTWARETYR B:64 , ARC B:1001 , ARC B:1002BINDING SITE FOR RESIDUE GOL B 1005
23CC5SOFTWARETYR A:64 , ARC A:1001 , LEU B:127 , GLC B:248 , ARC B:1003BINDING SITE FOR RESIDUE GOL A 1003
24CC6SOFTWARELEU A:127 , ARC A:1002 , TYR C:64 , GLC C:248 , ARC C:1002BINDING SITE FOR RESIDUE GOL C 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BRR)

(-) Sequences/Alignments

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:230
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:230
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
           BACR_HALSA    16 QITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245
               SCOP domains d1brra_ A: Bacteriorhodopsin                                                                                                                                                                                                           SCOP domains
               CATH domains 1brrA00 A:3-232 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brr A   3 QITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 232
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:231
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 
           BACR_HALSA    15 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245
               SCOP domains d1brrb_ B: Bacteriorhodopsin                                                                                                                                                                                                            SCOP domains
               CATH domains 1brrB00 B:2-232 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brr B   2 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 


Chain C from PDB  Type:PROTEIN  Length:232
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:232
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243  
           BACR_HALSA    14 QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245
               SCOP domains d1brrc_ C: Bacteriorhodopsin                                                                                                                                                                                                             SCOP domains
               CATH domains -1brrC00 C:2-232 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brr C   1 xAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 232
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
                            1-PCA
   Legend:   → Mismatch (orange background)
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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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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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  1brr
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  BACR_HALSA | P02945
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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 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 1qm8 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

(no "Related Entries Specified in the PDB File" available for 1BRR)