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(-) Description

Title :  CRYSTAL STRUCTURE OF HALORHODOPSIN FROM NATRONOMONAS PHARAONIS
 
Authors :  T. Kouyama
Date :  27 Sep 09  (Deposition) - 15 Dec 09  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Light-Driven Chloride Ion Pump, Trimeric Bacterioruberin- Protein Complex, Retinal Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kouyama, S. Kanada, Y. Takeguchi, A. Narusawa, M. Murakami, K. Ihara
Crystal Structure Of The Light-Driven Chloride Pump Halorhodopsin From Natronomonas Pharaonis.
J. Mol. Biol. V. 396 564 2010
PubMed-ID: 19961859  |  Reference-DOI: 10.1016/J.JMB.2009.11.061

(-) Compounds

Molecule 1 - HALORHODOPSIN
    Chains: A, B, D
    Organism Scientific: NATRONOMONAS PHARAONIS DSM 2160
    Organism Taxid: 348780
    Other Details: STRAIN MK-1 WAS A HALORHODOPSIN- OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T.

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric/Biological Unit (6, 30)
No.NameCountTypeFull Name
122B3Ligand/IonBACTERIORUBERIN
2CL6Ligand/IonCHLORIDE ION
3L1P3Ligand/Ion3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
4L2P6Ligand/Ion2,3-DI-PHYTANYL-GLYCEROL
5L3P9Ligand/Ion2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
6RET3Ligand/IonRETINAL

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:127 , THR A:131 , MET A:159 , TYR A:180 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , ASP A:252 , LYS A:256BINDING SITE FOR RESIDUE RET A 292
02AC2SOFTWARELEU A:29 , GLY A:46 , THR A:56 , LYS A:65 , ILE A:72 , THR D:151 , PHE D:155 , ALA D:185 , GLU D:197BINDING SITE FOR RESIDUE 22B A 300
03AC3SOFTWARELEU A:89 , HOH A:552 , SER D:92 , LEU D:94 , TRP D:121 , LEU D:125 , VAL D:161 , LEU D:164 , LEU D:168BINDING SITE FOR RESIDUE L1P A 293
04AC4SOFTWAREALA A:146 , PHE A:150 , ILE A:153 , THR A:154 , ILE A:157 , ALA A:158 , L2P A:295 , VAL B:77 , ALA B:80 , L2P B:295BINDING SITE FOR RESIDUE L2P A 294
05AC5SOFTWAREMET A:133 , LEU A:136 , ILE A:157 , L2P A:294 , L2P D:294BINDING SITE FOR RESIDUE L2P A 295
06AC6SOFTWARELEU A:195 , GLN A:200BINDING SITE FOR RESIDUE L3P A 331
07AC7SOFTWAREILE A:188 , TYR A:192BINDING SITE FOR RESIDUE L3P A 296
08AC8SOFTWARESER A:172 , LEU A:174 , PHE A:178 , PHE B:25 , ASN B:270BINDING SITE FOR RESIDUE L3P A 297
09AC9SOFTWARELEU A:29 , LEU D:174BINDING SITE FOR RESIDUE L3P A 298
10BC1SOFTWAREL2P B:295BINDING SITE FOR RESIDUE L3P A 299
11BC2SOFTWARETRP A:177 , TYR A:180 , CYS A:184BINDING SITE FOR RESIDUE L3P A 301
12BC3SOFTWARESER A:36 , VAL A:238 , LEU A:239 , TYR A:243 , TRP A:246 , ALA A:250BINDING SITE FOR RESIDUE L3P A 333
13BC4SOFTWARETHR A:126 , SER A:130 , LYS A:256BINDING SITE FOR RESIDUE CL A 401
14BC5SOFTWAREASN A:145 , PRO B:62 , HOH B:527 , HOH B:531BINDING SITE FOR RESIDUE CL A 402
15BC6SOFTWARETHR A:147 , THR A:151 , PHE A:155 , ALA A:185 , VAL A:189 , ALA B:43 , GLY B:46 , ILE B:49 , VAL B:53 , THR B:56 , ILE B:72 , VAL B:273 , HOH B:531BINDING SITE FOR RESIDUE 22B B 300
16BC7SOFTWARETYR B:180 , PHE D:54BINDING SITE FOR RESIDUE L3P B 331
17BC8SOFTWARETRP B:127 , THR B:131 , MET B:159 , TYR B:180 , SER B:183 , PHE B:187 , TRP B:222 , TYR B:225 , PRO B:226 , ASP B:252 , LYS B:256BINDING SITE FOR RESIDUE RET B 292
18BC9SOFTWARETHR B:126 , SER B:130 , LYS B:256 , HOH B:502BINDING SITE FOR RESIDUE CL B 401
19CC1SOFTWAREVAL A:19 , SER A:92 , VAL A:93 , LEU A:125 , VAL A:161 , ALA A:165 , VAL B:19 , ALA B:80 , LEU B:89 , THR B:90 , LEU B:125BINDING SITE FOR RESIDUE L1P B 293
20CC2SOFTWAREASN B:145BINDING SITE FOR RESIDUE CL B 402
21CC3SOFTWARESER B:92 , LEU B:94 , TRP B:121 , LEU B:125 , ILE B:157 , VAL B:161 , ALA B:165 , HOH B:541 , ALA D:80 , LEU D:89 , LEU D:125 , THR D:126BINDING SITE FOR RESIDUE L1P B 294
22CC4SOFTWAREPHE B:101 , THR B:147 , LYS B:148 , THR B:151 , PHE B:155 , ILE B:182 , ILE B:193 , GLU B:197 , ILE D:49 , THR D:56 , LYS D:65 , VAL D:69 , ILE D:72 , VAL D:76 , ILE D:79BINDING SITE FOR RESIDUE 22B D 300
23CC5SOFTWAREALA A:146 , PHE A:150 , L2P A:294 , L3P A:299 , ALA B:128 , LEU B:129 , MET B:133 , LEU B:136 , ILE B:153 , ILE B:157 , L2P B:296BINDING SITE FOR RESIDUE L2P B 295
24CC6SOFTWAREALA B:146 , PHE B:150 , ILE B:153 , THR B:154 , ILE B:157 , ALA B:158 , VAL B:161 , L2P B:295BINDING SITE FOR RESIDUE L2P B 296
25CC7SOFTWARELEU D:174BINDING SITE FOR RESIDUE L3P D 330
26CC8SOFTWARETRP D:127 , THR D:131 , MET D:159 , GLY D:163 , TYR D:180 , SER D:183 , TRP D:222 , TYR D:225 , PRO D:226 , TRP D:229 , ASP D:252 , LYS D:256BINDING SITE FOR RESIDUE RET D 292
27CC9SOFTWARETHR D:126 , TRP D:127 , SER D:130 , LYS D:256 , HOH D:502BINDING SITE FOR RESIDUE CL D 401
28DC1SOFTWAREPRO A:62 , LYS A:65 , ASN D:145 , LYS D:148BINDING SITE FOR RESIDUE CL D 402
29DC2SOFTWAREPHE B:150 , LEU D:66 , ALA D:128 , MET D:133 , LEU D:136 , ILE D:157BINDING SITE FOR RESIDUE L2P D 293
30DC3SOFTWAREL2P A:295 , SER D:144 , ALA D:146 , LEU D:149 , ILE D:153 , THR D:154 , ILE D:157BINDING SITE FOR RESIDUE L2P D 294

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A7K)

(-) Exons   (0, 0)

(no "Exon" information available for 3A7K)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d3a7ka_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3a7kA00 A:19-277 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7k A  19 VTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGS 277
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268         


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d3a7kb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3a7kB00 B:19-276 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eeehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a7k B  19 VTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSG 276
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268        


Chain D from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d3a7kd_ D: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3a7kD00 D:19-277 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......................eee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7k D  19 VTQRELFEFVLNDPLLASSLYINIALAGLSILLFVFMTRGLDDPRAKLIAVSTILVPVVSIASYTGLASGLTISVLEMPAGHFAEGSSVMLGGEEVDGVVTMWGRYLTWALSTPMILLALGLLAGSNATKLFTAITFDIAMCVTGLAAALTTSSHLMRWFWYAISCACFIVVLYILLVEWAQDAKAAGTADIFSTLKLLTVVMWLGYPIVWALGVEGVAVLPVGYTSWAYSALDIVAKYIFAFLLLNYLTSNEGVVSGS 277
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
   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 3A7K)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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3a4b CRYSTAL STRUCTURE OF THE SAME PROTEIN AT A LOWER RESOLUTION