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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF XANTHORHODOPSIN, A LIGHT-DRIVEN ION PUMP WITH DUAL CHROMOPHORE
 
Authors :  J. Stagno, H. Luecke, B. Schobert, J. K. Lanyi, E. S. Imasheva, J. M. Wang S. P. Balashov
Date :  05 Jun 08  (Deposition) - 14 Oct 08  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rhodopsin, Carotenoid, Ion Pump, Light-Harvesting, Antenna, Retinal, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Luecke, B. Schobert, J. Stagno, E. S. Imasheva, J. M. Wang, S. P. Balashov, J. K. Lanyi
Crystallographic Structure Of Xanthorhodopsin, The Light-Driven Proton Pump With A Dual Chromophore.
Proc. Natl. Acad. Sci. Usa V. 105 16561 2008
PubMed-ID: 18922772  |  Reference-DOI: 10.1073/PNAS.0807162105

(-) Compounds

Molecule 1 - XANTHORHODOPSIN
    Chains: A, B
    Organism Scientific: SALINIBACTER RUBER
    Organism Taxid: 146919

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric Unit (5, 27)
No.NameCountTypeFull Name
1PCW1Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2PX41Ligand/Ion1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3RET2Ligand/IonRETINAL
4SXN2Ligand/IonSALINIXANTHIN
5UNL21Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1PCW-1Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2PX4-1Ligand/Ion1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3RET1Ligand/IonRETINAL
4SXN1Ligand/IonSALINIXANTHIN
5UNL8Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (5, 17)
No.NameCountTypeFull Name
1PCW1Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2PX41Ligand/Ion1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3RET1Ligand/IonRETINAL
4SXN1Ligand/IonSALINIXANTHIN
5UNL13Ligand/IonUNKNOWN LIGAND

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:148 , GLY A:156 , THR A:160 , ARG A:184 , ASN A:191 , LEU A:194 , ALA A:198 , TYR A:207 , MET A:208 , MET A:211 , UNL A:1408BINDING SITE FOR RESIDUE SXN A1401
02AC2SOFTWAREMET A:19 , ILE A:234BINDING SITE FOR RESIDUE UNL A1402
03AC3SOFTWAREPRO A:139BINDING SITE FOR RESIDUE UNL A1403
04AC4SOFTWARELEU A:36 , LEU B:154BINDING SITE FOR RESIDUE UNL A1404
05AC5SOFTWARESER A:21 , PHE A:22 , UNL B:1403BINDING SITE FOR RESIDUE UNL A1405
06AC6SOFTWAREPHE A:202BINDING SITE FOR RESIDUE UNL A1406
07AC7SOFTWARETYR A:168 , PHE A:171BINDING SITE FOR RESIDUE UNL A1407
08AC8SOFTWAREGLY A:242 , ASN A:249 , SXN A:1401BINDING SITE FOR RESIDUE UNL A1408
09AC9SOFTWAREVAL A:164 , TYR A:168BINDING SITE FOR RESIDUE UNL A1409
10BC1SOFTWARETRP A:97 , VAL A:101 , MET A:133 , SER A:159 , PHE A:163 , TRP A:200 , TYR A:203 , ASP A:236 , ALA A:239 , LYS A:240BINDING SITE FOR RESIDUE RET A1301
11BC2SOFTWARELEU B:148 , GLY B:156 , THR B:160 , ARG B:184 , ASN B:191 , LEU B:194 , ALA B:198 , TYR B:207 , MET B:211 , PCW B:1416BINDING SITE FOR RESIDUE SXN B1401
12BC3SOFTWAREGLY A:11 , PRO B:102 , PHE B:128BINDING SITE FOR RESIDUE UNL B1402
13BC4SOFTWAREUNL A:1405 , LYS B:125 , TRP B:165BINDING SITE FOR RESIDUE UNL B1403
14BC5SOFTWARETHR B:28 , GLY B:60BINDING SITE FOR RESIDUE UNL B1404
15BC6SOFTWARELEU B:148 , GLY B:153 , LEU B:154BINDING SITE FOR RESIDUE UNL B1405
16BC7SOFTWAREPHE B:202BINDING SITE FOR RESIDUE UNL B1406
17BC8SOFTWARELEU B:197BINDING SITE FOR RESIDUE UNL B1408
18BC9SOFTWARELEU A:136 , VAL B:32 , UNL B:1412BINDING SITE FOR RESIDUE UNL B1409
19CC1SOFTWAREVAL B:164 , TRP B:165BINDING SITE FOR RESIDUE UNL B1410
20CC2SOFTWAREPX4 B:1415BINDING SITE FOR RESIDUE UNL B1411
21CC3SOFTWAREVAL B:24 , THR B:67 , GLU B:71 , UNL B:1409BINDING SITE FOR RESIDUE UNL B1412
22CC4SOFTWAREMET B:50 , PHE B:57BINDING SITE FOR RESIDUE UNL B1413
23CC5SOFTWARETRP B:97 , VAL B:101 , MET B:133 , SER B:159 , TRP B:200 , TYR B:203 , ASP B:236 , ALA B:239 , LYS B:240BINDING SITE FOR RESIDUE RET B1301
24CC6SOFTWAREVAL A:106 , GLY A:120 , ALA A:123 , PHE A:128 , THR B:9 , GLY B:11 , UNL B:1411 , PCW B:1416BINDING SITE FOR RESIDUE PX4 B1415
25CC7SOFTWAREGLY B:242 , LEU B:246 , SXN B:1401 , PX4 B:1415BINDING SITE FOR RESIDUE PCW B1416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DDL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DDL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DDL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DDL)

(-) Exons   (0, 0)

(no "Exon" information available for 3DDL)

(-) 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:252
 aligned with Q2S2F8_SALRD | Q2S2F8 from UniProtKB/TrEMBL  Length:273

    Alignment length:258
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253        
         Q2S2F8_SALRD     4 ELPTLTPGQYSLVFNMFSFTVATMTASFVFFVLARNNVAPKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKAKSEEEGFN 261
               SCOP domains d3ddla_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3ddlA00 A:4-261 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ddl A   4 ELPTLTPGQYSLVFNMFSFTVATMTASFVFFVLARNNVAPKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPM------PSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKAKSEEEGFN 261
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       | -    |  223       233       243       253        
                                                                                                                                                                                                                                         211    218                                           


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with Q2S2F8_SALRD | Q2S2F8 from UniProtKB/TrEMBL  Length:273

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
         Q2S2F8_SALRD     5 LPTLTPGQYSLVFNMFSFTVATMTASFVFFVLARNNVAPKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMAFPEAFPSNTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKAKSEEEGFN 261
               SCOP domains d3ddlb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3ddlB00 B:5-261 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddl B   5 LPTLTPGQYSLVFNMFSFTVATMTASFVFFVLARNNVAPKYRISMMVSALVVFIAGYHYFRITSSWEAAYALQNGMYQPTGELFNDAYRYVDWLLTVPLLTVELVLVMGLPKNERGPLAAKLGFLAALMIVLGYPGEVSENAALFGTRGLWGFLSTIPFVWILYILFTQLGDTIQRQSSRVSTLLGNARLLLLATWGFYPIAYMIPMA-------NTPGTIVALQVGYTIADVLAKAGYGVLIYNIAKAKSEEEGFN 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       | -     | 224       234       244       254       
                                                                                                                                                                                                                                         212     220
   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 3DDL)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2S2F8_SALRD | Q2S2F8)
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:0010461    light-activated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens in response to a light stimulus.
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.
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.

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