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(-) Description

Title :  M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE
 
Authors :  H. J. Sass, J. Berendzen, D. Neff, R. Gessenich, P. Ormos, G. Bueldt
Date :  26 Aug 99  (Deposition) - 20 Oct 99  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Photo Cycle Intermediate, 7-Helical Membrane Protein, Proton Transport, Retinal Protein, Ion Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Sass, G. Buldt, R. Gessenich, D. Hehn, D. Neff, R. Schlesinger, J. Berendzen, P. Ormos
Structural Alterations For Proton Translocation In The M State Of Wild-Type Bacteriorhodopsin.
Nature V. 406 649 2000
PubMed-ID: 10949308  |  Reference-DOI: 10.1038/35020607

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)
    Cellular Location: TRANSMEMBRANE
    Chains: A, B
    Engineered: YES
    Expression System: HALOBACTERIUM SALINARUM
    Expression System Taxid: 2242
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Other Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 601 (C15) DIETHER LIPID BILAYER

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 44)

Asymmetric Unit (5, 44)
No.NameCountTypeFull Name
1HEX12Ligand/IonHEXANE
2OCT16Ligand/IonN-OCTANE
3RET2Ligand/IonRETINAL
4TRD6Ligand/IonTRIDECANE
5UND8Ligand/IonUNDECANE
Biological Unit 1 (5, 132)
No.NameCountTypeFull Name
1HEX36Ligand/IonHEXANE
2OCT48Ligand/IonN-OCTANE
3RET6Ligand/IonRETINAL
4TRD18Ligand/IonTRIDECANE
5UND24Ligand/IonUNDECANE

(-) Sites  (44, 44)

Asymmetric Unit (44, 44)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:86 , THR A:90 , LEU A:93 , MET A:118 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , ASP A:212 , LYS A:216 , TYR B:83 , TRP B:86 , THR B:89 , SER B:141 , THR B:142 , TRP B:182 , TYR B:185 , PRO B:186 , ASP B:212 , ALA B:215 , LYS B:216 , RET B:601BINDING SITE FOR RESIDUE RET A 601
02AC2SOFTWARETRP A:86 , THR A:89 , THR A:90 , LEU A:93 , MET A:118 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , PRO A:186 , TRP A:189 , LYS A:216 , RET A:601 , TYR B:83 , TRP B:86 , THR B:89 , MET B:118 , ILE B:119 , TRP B:138 , SER B:141 , THR B:142 , TRP B:182 , TYR B:185 , PRO B:186 , ALA B:215 , LYS B:216BINDING SITE FOR RESIDUE RET B 601
03AC3SOFTWARELEU A:146 , TYR A:147 , PHE A:154 , VAL A:173 , ILE A:222 , UND A:1604 , LEU B:146 , TYR B:147 , TYR B:150 , PHE B:154BINDING SITE FOR RESIDUE UND A 604
04AC4SOFTWAREPHE A:135 , ALA A:139 , HEX A:606 , OCT A:623 , OCT A:1605 , HEX A:1606 , PHE B:135 , VAL B:136 , ALA B:139BINDING SITE FOR RESIDUE OCT A 605
05AC5SOFTWARELEU A:15 , VAL A:210 , OCT A:605 , UND A:624 , HEX A:1606 , UND A:1624BINDING SITE FOR RESIDUE HEX A 606
06AC6SOFTWAREILE A:52 , PHE A:88 , GLY A:116 , ILE B:52 , PHE B:88 , GLY B:113 , ILE B:117 , OCT B:1607BINDING SITE FOR RESIDUE OCT B 607
07AC7SOFTWAREVAL A:217 , HEX A:1608 , VAL B:217 , UND B:1614BINDING SITE FOR RESIDUE HEX A 608
08AC8SOFTWAREARG B:175 , ASN B:176 , OCT B:1609BINDING SITE FOR RESIDUE OCT B 609
09AC9SOFTWARELEU A:87 , VAL A:112 , HEX A:1610 , VAL B:112BINDING SITE FOR RESIDUE HEX A 610
10BC1SOFTWAREGLY A:21 , THR A:47 , LEU A:48 , PHE A:54 , ALA A:110 , TYR A:147 , HOH A:871 , GLY B:21 , THR B:24 , ALA B:44 , LEU B:48 , PHE B:54 , ALA B:110 , ILE B:140 , ALA B:144 , TYR B:147 , TRD B:1611BINDING SITE FOR RESIDUE TRD B 611
11BC2SOFTWARELEU A:28 , OCT A:623 , TRD A:1612BINDING SITE FOR RESIDUE TRD A 612
12BC3SOFTWARELEU A:22 , LEU B:22 , UND B:614 , OCT B:1613BINDING SITE FOR RESIDUE OCT B 613
13BC4SOFTWARELEU A:25 , VAL A:29 , LEU B:25 , VAL B:29 , OCT B:613 , OCT B:1613 , UND B:1614BINDING SITE FOR RESIDUE UND B 614
14BC5SOFTWARELYS A:41 , LEU A:95 , LEU A:99 , HEX A:1610 , TRD A:1615 , PRO B:91 , GLN B:105BINDING SITE FOR RESIDUE TRD B 615
15BC6SOFTWAREILE A:198 , ILE B:198 , UND B:1616BINDING SITE FOR RESIDUE UND B 616
16BC7SOFTWAREUND A:1604 , OCT A:1617BINDING SITE FOR RESIDUE OCT A 617
17BC8SOFTWARETRP A:138 , LEU A:190 , HEX A:620 , OCT A:1617 , TRP B:138 , LEU B:190 , UND B:1616 , OCT B:1618 , HEX B:1620BINDING SITE FOR RESIDUE OCT B 618
18BC9SOFTWARETYR A:26 , VAL A:29 , VAL B:29 , HEX B:1619BINDING SITE FOR RESIDUE HEX B 619
19CC1SOFTWARELEU A:146 , SER A:183 , VAL A:187 , OCT A:1617 , MET B:145 , SER B:183 , VAL B:187 , OCT B:618 , HEX B:1620BINDING SITE FOR RESIDUE HEX A 620
20CC2SOFTWAREOCT A:1621BINDING SITE FOR RESIDUE OCT B 621
21CC3SOFTWARETRP A:80 , HEX A:1622 , TRP B:80 , HOH B:821BINDING SITE FOR RESIDUE HEX B 622
22CC4SOFTWAREPHE A:135 , TRP A:138 , LEU A:206 , OCT A:605 , TRD A:612 , OCT A:1605 , OCT A:1623 , PHE B:135 , TRP B:138 , ILE B:203 , HOH B:803 , HOH B:1803BINDING SITE FOR RESIDUE OCT A 623
23CC5SOFTWAREHEX A:606 , HEX A:1606 , UND A:1624BINDING SITE FOR RESIDUE UND A 624
24CC6SOFTWAREVAL A:173 , VAL A:177 , ILE A:222 , UND A:604 , OCT A:617 , TRD A:1612 , OCT A:1617 , LEU B:146 , TYR B:147 , VAL B:173 , ILE B:222BINDING SITE FOR RESIDUE UND A 1604
25CC7SOFTWARETRP A:12 , SER A:132 , LEU A:206 , OCT A:605 , OCT A:623 , HOH A:854 , TRP B:12 , SER B:132 , PHE B:135BINDING SITE FOR RESIDUE OCT A 1605
26CC8SOFTWARETRP A:12 , LEU A:15 , OCT A:605 , HEX A:606 , UND A:624 , TRP B:12BINDING SITE FOR RESIDUE HEX A 1606
27CC9SOFTWAREILE A:52 , GLY A:113 , GLY A:116 , ILE A:117 , ILE B:52 , PHE B:88 , GLY B:113 , GLY B:116 , ILE B:117 , OCT B:607BINDING SITE FOR RESIDUE OCT B 1607
28DC1SOFTWARELEU A:19 , GLY A:23 , HEX A:608 , LEU B:19 , GLY B:23 , TYR B:26BINDING SITE FOR RESIDUE HEX A 1608
29DC2SOFTWAREOCT B:609BINDING SITE FOR RESIDUE OCT B 1609
30DC3SOFTWARELEU A:87 , VAL A:112 , HEX A:610 , TRD A:1615 , VAL B:112 , TRD B:615BINDING SITE FOR RESIDUE HEX A 1610
31DC4SOFTWARETHR A:47 , TYR A:147 , HOH A:871 , HOH A:1872 , LEU B:48 , PHE B:54 , TYR B:147 , TRD B:611BINDING SITE FOR RESIDUE TRD B 1611
32DC5SOFTWARELEU A:28 , MET A:32 , LEU A:146 , TRD A:612 , UND A:1604 , LEU B:146BINDING SITE FOR RESIDUE TRD A 1612
33DC6SOFTWARELEU A:22 , LEU B:22 , OCT B:613 , UND B:614BINDING SITE FOR RESIDUE OCT B 1613
34DC7SOFTWARELEU A:19 , HEX A:608 , LEU B:19 , LEU B:25 , VAL B:29 , UND B:614BINDING SITE FOR RESIDUE UND B 1614
35DC8SOFTWARELEU A:99 , GLN A:105 , ILE A:108 , HEX A:1610 , PRO B:91 , LEU B:92 , GLN B:105 , ILE B:108 , TRD B:615BINDING SITE FOR RESIDUE TRD A 1615
36DC9SOFTWAREILE B:198 , UND B:616 , OCT B:618BINDING SITE FOR RESIDUE UND B 1616
37EC1SOFTWAREASN A:176 , OCT A:617 , HEX A:620 , UND A:1604 , OCT B:618BINDING SITE FOR RESIDUE OCT A 1617
38EC2SOFTWAREOCT A:1623 , TRP B:138 , LEU B:190 , OCT B:618BINDING SITE FOR RESIDUE OCT B 1618
39EC3SOFTWARETYR A:26 , TYR B:26 , VAL B:29 , HEX B:619BINDING SITE FOR RESIDUE HEX B 1619
40EC4SOFTWARETHR A:142 , SER A:183 , HEX A:620 , THR B:142 , MET B:145 , SER B:183 , OCT B:618BINDING SITE FOR RESIDUE HEX B 1620
41EC5SOFTWAREOCT B:621BINDING SITE FOR RESIDUE OCT A 1621
42EC6SOFTWARELEU A:123 , LEU B:123 , HEX B:622BINDING SITE FOR RESIDUE HEX A 1622
43EC7SOFTWAREILE A:203 , LEU A:207 , OCT A:623 , PHE B:135 , ILE B:203 , LEU B:206 , LEU B:207 , HOH B:803 , OCT B:1618 , HOH B:1803BINDING SITE FOR RESIDUE OCT A 1623
44EC8SOFTWAREVAL A:136 , HEX A:606 , UND A:624BINDING SITE FOR RESIDUE UND A 1624

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107
 		  2A:82-94
B:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232
 		  2A:208-219
B:208-219
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107
 		  6A:82-94
B:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232
 		  6A:208-219
B:208-219

(-) Exons   (0, 0)

(no "Exon" information available for 1CWQ)

(-) 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:238
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:238
                                    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 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPS 252
               SCOP domains d1cwqa_ A: Bacteriorhodopsin                                                                                                                                                                                                                   SCOP domains
               CATH domains 1cwqA00 A:2-239 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP-------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cwq A   2 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPS 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:238
                                    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 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPS 252
               SCOP domains d1cwqb_ B: Bacteriorhodopsin                                                                                                                                                                                                                   SCOP domains
               CATH domains 1cwqB00 B:2-239 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP-------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cwq B   2 AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPS 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  1cwq
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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 1brr 1brx 1c3w 1c8r 1c8s 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

1c3w GROUND STATE STRUCTURE AT 1.55 A
1c8r GROUND STATE OF D96N MUTANT
1c8s M INTERMEDIATE OF D96N MUTANT