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(-) Description

Title :  CRYSTAL STRUCTURE OF EXIGUOBACTERIUM SIBIRICUM RHODOPSIN
 
Authors :  I. Gushchin, P. Chervakov, P. Kuzmichev, A. Popov, E. Round, V. Borshch D. Dolgikh, M. Kirpichnikov, L. Petrovskaya, V. Chupin, A. Arseniev, V. Gordeliy
Date :  13 Nov 12  (Deposition) - 17 Jul 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Seven-Helical Transmembrane Protein, Proton Pump, Membrane, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Gushchin, P. Chervakov, P. Kuzmichev, A. N. Popov, E. Round, V. Borshchevskiy, A. Ishchenko, L. Petrovskaya, V. Chupin, D. A. Dolgikh, A. A. Arseniev, M. Kirpichnikov, V. Gordeliy
Structural Insights Into The Proton Pumping By Unusual Proteorhodopsin From Nonmarine Bacteria.
Proc. Natl. Acad. Sci. Usa V. 110 12631 2013
PubMed-ID: 23872846  |  Reference-DOI: 10.1073/PNAS.1221629110

(-) Compounds

Molecule 1 - RHODOPSIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EXIG_1419
    Organism Scientific: EXIGUOBACTERIUM SIBIRICUM
    Organism Taxid: 332410

 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  (2, 32)

Asymmetric Unit (2, 32)
No.NameCountTypeFull Name
1LFA30Ligand/IonEICOSANE
2RET2Ligand/IonRETINAL
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1LFA12Ligand/IonEICOSANE
2RET1Ligand/IonRETINAL
Biological Unit 2 (2, 19)
No.NameCountTypeFull Name
1LFA18Ligand/IonEICOSANE
2RET1Ligand/IonRETINAL

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:83 , TRP A:86 , MET A:122 , GLY A:126 , TYR A:147 , GLY A:150 , CYS A:151 , TRP A:154 , TRP A:191 , TYR A:194 , PRO A:195 , TYR A:198 , LYS A:225BINDING SITE FOR RESIDUE RET A 301
02AC2SOFTWARELFA A:308BINDING SITE FOR RESIDUE LFA A 302
03AC3SOFTWAREPRO A:38 , THR A:45 , LEU A:49 , LFA A:305 , VAL B:53 , PHE B:60 , ILE B:81 , ILE B:84BINDING SITE FOR RESIDUE LFA A 304
04AC4SOFTWAREVAL A:88 , LFA A:304 , LEU B:49BINDING SITE FOR RESIDUE LFA A 305
05AC5SOFTWARELYS A:114 , ILE A:117 , PHE A:152 , TYR A:156 , LFA A:312BINDING SITE FOR RESIDUE LFA A 306
06AC6SOFTWAREPHE A:186BINDING SITE FOR RESIDUE LFA A 307
07AC7SOFTWAREVAL A:212 , LFA A:302BINDING SITE FOR RESIDUE LFA A 308
08AC8SOFTWARELYS A:62BINDING SITE FOR RESIDUE LFA A 310
09AC9SOFTWAREVAL A:124 , LFA B:317BINDING SITE FOR RESIDUE LFA A 311
10BC1SOFTWARELFA A:306BINDING SITE FOR RESIDUE LFA A 312
11BC2SOFTWAREILE A:193 , ILE A:216BINDING SITE FOR RESIDUE LFA A 313
12BC3SOFTWARETYR B:83 , TRP B:86 , THR B:90 , MET B:122 , GLY B:126 , TYR B:147 , GLY B:150 , CYS B:151 , TRP B:191 , TYR B:194 , ASP B:221 , LYS B:225BINDING SITE FOR RESIDUE RET B 301
13BC4SOFTWARELEU A:92 , VAL A:95 , GLU B:80 , ILE B:84BINDING SITE FOR RESIDUE LFA B 302
14BC5SOFTWARETHR B:45BINDING SITE FOR RESIDUE LFA B 303
15BC6SOFTWARELYS B:62BINDING SITE FOR RESIDUE LFA B 304
16BC7SOFTWAREILE A:158 , PHE A:162 , THR A:163 , LFA B:319BINDING SITE FOR RESIDUE LFA B 305
17BC8SOFTWARELEU B:27BINDING SITE FOR RESIDUE LFA B 306
18BC9SOFTWAREPHE A:203 , LFA B:308 , LFA B:310BINDING SITE FOR RESIDUE LFA B 307
19CC1SOFTWAREPHE A:139 , PHE A:203 , LFA B:307BINDING SITE FOR RESIDUE LFA B 308
20CC2SOFTWAREGLU A:80 , TYR A:127 , VAL B:95 , LEU B:103 , ARG B:109BINDING SITE FOR RESIDUE LFA B 309
21CC3SOFTWARELEU B:185 , LFA B:307BINDING SITE FOR RESIDUE LFA B 310
22CC4SOFTWARETHR B:223BINDING SITE FOR RESIDUE LFA B 311
23CC5SOFTWAREGLN B:141 , TRP B:145BINDING SITE FOR RESIDUE LFA B 312
24CC6SOFTWAREPHE A:152 , GLN B:141 , TRP B:145BINDING SITE FOR RESIDUE LFA B 313
25CC7SOFTWAREPHE B:52 , TYR B:59BINDING SITE FOR RESIDUE LFA B 314
26CC8SOFTWARETYR B:156BINDING SITE FOR RESIDUE LFA B 315
27CC9SOFTWAREPHE A:234 , TYR B:13 , LFA B:318BINDING SITE FOR RESIDUE LFA B 316
28DC1SOFTWARELFA A:311 , ILE B:121BINDING SITE FOR RESIDUE LFA B 317
29DC2SOFTWARETYR A:28 , LEU A:230 , TRP B:16 , VAL B:20 , LFA B:316BINDING SITE FOR RESIDUE LFA B 318
30DC3SOFTWARELFA B:305BINDING SITE FOR RESIDUE LFA B 319

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HYJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HYJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HYJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HYJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4HYJ)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains d4hyja_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyj A   3 EVNLLVLATQYMFWVGFVGMAAGTLYFLVERNSLAPEYRSTATVAALVTFVAAIHYYFMKDAVGTSGLLSEIDGFPTEIRYIDWLVTTPLLLVKFPLLLGRLGRPLLTKLVIADVIMIVGGYIGESSINIAGGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRDALLKMRLFILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFFAVKTMSS 241
                                    12        22        32        42        52        62        72        82        92       102|      115       125       135       145       155       165       175       185       195       205       215       225       235      
                                                                                                                             102|                                                                                                                                       
                                                                                                                              106                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains d4hyjb_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyj B   7 LVLATQYMFWVGFVGMAAGTLYFLVERNSLAPEYRSTATVAALVTFVAAIHYYFMKDFPTEIRYIDWLVTTPLLLVKFPLLLGLKGRLGRPLLTKLVIADVIMIVGGYIGESSINIAGGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRDALLKMRLFILIGWAIYPIGYAVTLFAPGVEIQLVRELIYNFADLTNKVGFGLIAFFAVKTMSSLS 243
                                    16        26        36        46        56      ||79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
                                                                                   63|                                                                                                                                                                      
                                                                                    77
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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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HYJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HYJ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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