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(-) Description

Title :  CRYSTAL STRUCTURE OF ORANGE CAROTENOID PROTEIN WITH PARTIAL LOSS OF 3'OH ECHINENONE CHROMOPHORE
 
Authors :  X. Yang, S. Bandara, Z. Ren
Date :  07 Nov 16  (Deposition) - 07 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Photoreceptor, Photoprotection, Dynamic Crystallography, Carotenoid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bandara, Z. Ren, L. Lu, X. Zeng, H. Shin, K. H. Zhao, X. Yang
Photoactivation Mechanism Of A Carotenoid-Based Photoreceptor.
Proc. Natl. Acad. Sci. V. 114 6286 2017 U. S. A.
PubMed-ID: 28559328  |  Reference-DOI: 10.1073/PNAS.1700956114

(-) Compounds

Molecule 1 - ORANGE CAROTENOID-BINDING PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: SYNECHOCYSTIS SP. PCC 6803
    Expression System Taxid: 1148
    Gene: SLR1963
    Organism Scientific: SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KAZUSA)
    Organism Taxid: 1111708
    Strain: PCC 6803 / KAZUSA
    Synonym: OCP

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1EQ36Ligand/Ion(3'R)-3'-HYDROXY-BETA,BETA-CAROTEN-4-ONE
2GOL4Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:55 , PRO A:56 , GLU A:174 , ASN A:247 , TRP A:277binding site for residue GOL A 401
02AC2SOFTWARELEU A:37 , ILE A:40 , TRP A:41 , TYR A:44 , LEU A:107 , TRP A:110 , TYR A:111 , GLY A:114 , ILE A:151 , THR A:152 , ARG A:155 , TYR A:201 , LEU A:205 , CYS A:245 , LEU A:250 , VAL A:273 , MET A:284 , TRP A:288 , ILE A:303binding site for residue EQ3 A 402
03AC3SOFTWARELEU B:37 , ILE B:40 , TRP B:41 , TYR B:44 , LEU B:107 , TRP B:110 , TYR B:111 , GLY B:114 , MET B:117 , ILE B:151 , THR B:152 , ARG B:155 , VAL B:158 , TYR B:201 , LEU B:205 , CYS B:245 , LEU B:250 , VAL B:273 , TRP B:277 , PHE B:278 , MET B:284 , TRP B:288binding site for residue EQ3 B 401
04AC4SOFTWAREALA C:55 , PRO C:56 , GLY C:57 , ASN C:104 , GLU C:174 , TRP C:277binding site for residue GOL C 401
05AC5SOFTWARETRP C:41 , PHE C:42 , ILE C:125 , PRO C:126 , ALA C:127 , GLY C:128 , PRO F:259 , ALA F:260 , GLU F:261binding site for residue GOL C 402
06AC6SOFTWARELEU C:37 , ILE C:40 , TRP C:41 , TYR C:44 , LEU C:107 , TRP C:110 , TYR C:111 , GLY C:114 , THR C:152 , ARG C:155 , VAL C:158 , TYR C:201 , LEU C:205 , CYS C:245 , LEU C:250 , VAL C:273 , TRP C:288binding site for residue EQ3 C 403
07AC7SOFTWARELEU D:37 , ILE D:40 , TRP D:41 , TYR D:44 , LEU D:107 , TRP D:110 , TYR D:111 , GLY D:114 , THR D:152 , ARG D:155 , VAL D:158 , TYR D:201 , LEU D:205 , CYS D:245 , LEU D:250 , VAL D:273 , TRP D:277 , MET D:284 , TRP D:288binding site for residue EQ3 D 401
08AC8SOFTWAREALA E:54 , ALA E:55 , PRO E:56 , GLY E:57 , ASN E:104 , GLU E:174 , TRP E:277binding site for residue GOL E 401
09AC9SOFTWARELEU E:37 , ILE E:40 , TRP E:41 , TYR E:44 , TRP E:110 , TYR E:111 , GLY E:114 , MET E:117 , ILE E:151 , THR E:152 , ARG E:155 , VAL E:158 , TYR E:201 , CYS E:245 , LEU E:250 , VAL E:273 , TRP E:277 , PHE E:278 , TRP E:288 , ILE E:303binding site for residue EQ3 E 402
10AD1SOFTWARELEU F:37 , ILE F:40 , TRP F:41 , TYR F:44 , ILE F:53 , LEU F:107 , TRP F:110 , TYR F:111 , GLY F:114 , ILE F:151 , THR F:152 , ARG F:155 , VAL F:158 , TYR F:201 , LEU F:205 , CYS F:245 , LEU F:250 , VAL F:273 , THR F:275 , TRP F:277 , MET F:284 , TRP F:288binding site for residue EQ3 F 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TUW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe C:163 -Thr C:164
2Gly C:169 -Lys C:170
3Phe E:163 -Thr E:164
4Phe F:163 -Thr F:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TUW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TUW)

(-) Exons   (0, 0)

(no "Exon" information available for 5TUW)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tuw A   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    176       186       196       206       216       226       236       246       256       266       276       286       296       306     
                                                                                                                                                                                           164|                                                                                                                                              
                                                                                                                                                                                            169                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tuw B   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    177       187       197       207       217       227       237       247       257       267       277       287       297       307    
                                                                                                                                                                                           164|                                                                                                                                             
                                                                                                                                                                                            170                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tuw C   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    176       186       196       206       216       226       236       246       256       266       276       286       296       306     
                                                                                                                                                                                           164|                                                                                                                                              
                                                                                                                                                                                            169                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tuw D   2 PFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  ||   175       185       195       205       215       225       235       245       255       265       275       285       295       305      
                                                                                                                                                                                            164|                                                                                                                                              
                                                                                                                                                                                             169                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tuw E   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    176       186       196       206       216       226       236       246       256       266       276       286       296       306     
                                                                                                                                                                                           164|                                                                                                                                              
                                                                                                                                                                                            169                                                                                                                                              


Chain F from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tuw F   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    176       186       196       206       216       226       236       246       256       266       276       286       296       306     
                                                                                                                                                                                           164|                                                                                                                                              
                                                                                                                                                                                            169
   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  (0, 0)

(no "SCOP Domain" information available for 5TUW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TUW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TUW)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OCP_SYNY3 | P74102: 3mg1 3mg2 3mg3 4xb4 4xb5 5tux 5tv0

(-) Related Entries Specified in the PDB File

5tux 5tv0