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(-) Description

Title :  CRYSTAL STRUCTURE OF A BLUE-LIGHT ABSORBING PROTEORHODOPSIN MUTANT D97N FROM HOT75
 
Authors :  T. Ran, G. Ozorowski, Y. Gao, W. Wang, H. Luecke
Date :  07 May 13  (Deposition) - 05 Jun 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Ion Transport, Proton Pump, Retinylidene Schiff Base, Membrane, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ran, G. Ozorowski, Y. Gao, O. A. Sineshchekov, W. Wang, J. L. Spudich H. Luecke
Cross-Protomer Interaction With The Photoactive Site In Oligomeric Proteorhodopsin Complexes.
Acta Crystallogr. , Sect. D V. 69 1965 2013
PubMed-ID: 24100316  |  Reference-DOI: 10.1107/S0907444913017575

(-) Compounds

Molecule 1 - BLUE-LIGHT ABSORBING PROTEORHODOPSIN
    Chains: A, B, C, D, E
    Mutation: YES
    Organism Scientific: GAMMA PROTEOBACTERIUM 'HOT 75M4'
    Organism Taxid: 245185
    Synonym: BPR

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 55)

Asymmetric/Biological Unit (2, 55)
No.NameCountTypeFull Name
1MSE50Mod. Amino AcidSELENOMETHIONINE
2RET5Ligand/IonRETINAL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:98 , THR A:101 , VAL A:102 , MSE A:134 , TRP A:159 , TRP A:197 , TYR A:200 , TYR A:204 , TYR A:224 , ASP A:228 , LYS A:232BINDING SITE FOR RESIDUE RET A 301
2AC2SOFTWARETRP B:98 , THR B:101 , VAL B:102 , GLN B:105 , MSE B:134 , TRP B:197 , TYR B:200 , TYR B:204 , TYR B:224 , LYS B:232BINDING SITE FOR RESIDUE RET B 301
3AC3SOFTWARETRP C:98 , THR C:101 , VAL C:102 , MSE C:134 , GLY C:138 , TRP C:159 , TRP C:197 , TYR C:200 , PRO C:201 , LYS C:232BINDING SITE FOR RESIDUE RET C 301
4AC4SOFTWARETRP D:98 , THR D:101 , VAL D:102 , GLN D:105 , MSE D:134 , GLY D:138 , PHE D:152 , TRP D:197 , TYR D:200 , TYR D:204 , TYR D:224 , LYS D:232BINDING SITE FOR RESIDUE RET D 301
5AC5SOFTWARETRP E:98 , THR E:101 , MSE E:134 , TRP E:159 , TRP E:197 , TYR E:200 , TYR E:224 , LYS E:232BINDING SITE FOR RESIDUE RET E 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu D:170 -Gly D:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KLY)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains d4klya_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kly A  21 GDLDISDTVGVSFWLVTAGmLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYmRGVWIDTGDTPTVFRYINWLLTVPLQVVEFYLILAACTSVAASLFKKLLAGSLVmLGAGFAGEAGLAPVLPAFIIGmAGWLYmIYELYmGEGKTASPAVNSAYNAmmmIIVVGWAIYPAGYAAGYLmGGGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNALEH 253
                                    30        40        50        60        70        80        90       100       110       120       130   |   140       150     | 160 |     170 ||    184    |||194       204     | 215       225       235       245        
                                              40-MSE                                 79-MSE                                                134-MSE               156-MSE |     | 172|         189-MSE              210-MSE                                      
                                                                                                                                                                       162-MSE |  177          190-MSE               212|                                       
                                                                                                                                                                             168-MSE            191-MSE               214                                       


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4klyb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kly B  21 GDLDISDTVGVSFWLVTAGmLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYmRGVWIDTGDTPTVFRYINWLLTVPLQVVEFYLILAACTSVAASLFKKLLAGSLVmLGAGFAGEAGLAPVLPAFIIGmAGWLYmIYELYmGEGKAAVSTASPAVNSAYNAmmmIIVVGWAIYPAGYAAGYLmGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNALEHHH 255
                                    30        40        50        60        70        80        90       100       110       120       130   |   140       150     | 160 |     170       180       190|      200       210||     223       233       243       253  
                                              40-MSE                                 79-MSE                                                134-MSE               156-MSE |     |                  189-MSE              210-MSE                                      
                                                                                                                                                                       162-MSE |                   190-MSE              211|                                        
                                                                                                                                                                             168-MSE                191-MSE              215                                        


Chain C from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains d4klyc_ C: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kly C  21 GDLDISDTVGVSFWLVTAGmLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYmRGVWIDTGDTPTVFRYINWLLTVPLQVVEFYLILAACTSVAASLFKKLLAGSLVmLGAGFAGEAGLAPVLPAFIIGmAGWLYmIYELYmGEGKAAVSTASPAVNSAYNAmmmIIVVGWAIYPAGYAAGYLmGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNALEH 253
                                    30        40        50        60        70        80        90       100       110       120       130   |   140       150     | 160 |     170       180       190|      200       210||     223       233       243       253
                                              40-MSE                                 79-MSE                                                134-MSE               156-MSE |     |                  189-MSE              210-MSE                                    
                                                                                                                                                                       162-MSE |                   190-MSE              211|                                      
                                                                                                                                                                             168-MSE                191-MSE              215                                      


Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains d4klyd_ D: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kly D  20 GGDLDISDTVGVSFWLVTAGmLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYmRGVWIDTGDTPTVFRYINWLLTVPLQVVEFYLILASVAASLFKKLLAGSLVmLGAGFAGEAGLAPVLPAFIIGmAGWLYmIYELYmGEGSPAVNSAYNAmmmIIVVGWAIYPAGYAAGYLmGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNALEH 253
                                    29        39|       49        59        69        79        89        99       109    || 122       132 |     142       152   |   162     | 179       189||     199       209|||    222       232       242       252 
                                               40-MSE                                 79-MSE                            114|             134-MSE               156-MSE |     |  ||       189-MSE              210-MSE                                    
                                                                                                                         118                                         162-MSE |  ||        190-MSE              211|                                      
                                                                                                                                                                           168-MSE         191-MSE              215                                      
                                                                                                                                                                              171|                                                                       
                                                                                                                                                                               179                                                                       


Chain E from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains d4klye_ E: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kly E  21 GDLDISDTVGVSFWLVTAGmLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYmRGVWIDTGDTPTVFRYINWLLTVPLQVVEFYLILAACTSVAASLFKKLLAGSLVmLGAGFAGEAGLAPVLPAFIIGmAGWLYmIYELYmGEGKTASPAVNSAYNAmmmIIVVGWAIYPAGYAAGYLmGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNALEH 253
                                    30        40        50        60        70        80        90       100       110       120       130   |   140       150     | 160 |     170 ||    184    |||194       204     ||217       227       237       247      
                                              40-MSE                                 79-MSE                                                134-MSE               156-MSE |     | 172|         189-MSE              210-MSE                                    
                                                                                                                                                                       162-MSE |  177          190-MSE              211|                                      
                                                                                                                                                                             168-MSE            191-MSE              215
   Legend:   → Mismatch (orange background)
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    → 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, 5)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        PRRB_PRB02 | Q9AFF7: 4knf

(-) Related Entries Specified in the PDB File

4jq6 4knf