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(-) Description

Title :  IRISFP FLUORESCENT PROTEIN IN ITS RED FORM, CIS CONFORMATION
 
Authors :  V. Adam, M. Lelimousin, S. Boehme, G. Desfonds, K. Nienhaus, M. J. Field, J. Wiedenmann, S. Mcsweeney, G. U. Nienhaus, D. Bourgeois
Date :  09 Jun 08  (Deposition) - 12 Aug 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Photoactivation, Photoconversion, Fluorescent Protein, Optical Highlighters, Microspectrophotometry, Eosfp, Photochromism, Photoswitching (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Adam, M. Lelimousin, S. Boehme, G. Desfonds, K. Nienhaus, M. J. Field, J. Wiedenmann, S. Mcsweeney, G. U. Nienhaus, D. Bourgeois
Structural Characterization Of Irisfp, An Optical Highlighter Undergoing Multiple Photo-Induced Transformations.
Proc. Natl. Acad. Sci. Usa V. 105 18343 2008
PubMed-ID: 19017808  |  Reference-DOI: 10.1073/PNAS.0805949105

(-) Compounds

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE32
    Expression System Strain: M15PREP4
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: LOBOPHYLLIA HEMPRICHII
    Organism Taxid: 46758
    Synonym: EOSFP

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1IEY4Mod. Amino Acid2-((1E)-2-(5-IMIDAZOLYL)ETHENYL)-4-(P-HYDROXYBENZYLIDENE)-5-IMIDAZOLINONE
2NFA4Mod. Amino AcidPHENYLALANINE AMIDE
3SO34Ligand/IonSULFITE ION
4SO415Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:17 , HIS A:22 , HIS A:121 , HOH A:2277 , HOH A:2279 , HOH A:2280 , HOH A:2281 , ARG C:119BINDING SITE FOR RESIDUE SO4 A1223
02AC2SOFTWAREALA A:167 , ARG B:149 , ASP B:150 , HOH B:2145 , HOH B:2217 , HOH B:2218BINDING SITE FOR RESIDUE SO4 B1224
03AC3SOFTWAREASP A:202 , LYS A:203 , HOH A:2282BINDING SITE FOR RESIDUE SO4 A1224
04AC4SOFTWARELYS A:182 , GLY A:183BINDING SITE FOR RESIDUE SO4 A1225
05AC5SOFTWARECYS A:195 , ILE A:196 , GLU A:197 , TYR A:211 , HOH A:2243 , HOH A:2283BINDING SITE FOR RESIDUE SO3 A1226
06AC6SOFTWAREASN B:17 , HIS B:22 , HIS B:121 , HOH B:2219 , HOH B:2220 , HOH B:2221 , HOH D:2122BINDING SITE FOR RESIDUE SO4 B1225
07AC7SOFTWAREARG A:149 , ASP A:150 , HOH A:2200 , HOH A:2284 , ALA B:167 , HOH B:2154BINDING SITE FOR RESIDUE SO4 A1227
08AC8SOFTWAREASP B:202 , LYS B:203 , HOH B:2222BINDING SITE FOR RESIDUE SO4 B1226
09AC9SOFTWARELYS B:182 , GLY B:183 , HOH B:2173BINDING SITE FOR RESIDUE SO4 B1227
10BC1SOFTWARECYS B:195 , ILE B:196 , GLU B:197 , TYR B:211 , HOH B:2223BINDING SITE FOR RESIDUE SO3 B1228
11BC2SOFTWAREASN C:17 , HIS C:22 , HIS C:121 , HOH C:2223 , HOH C:2224 , HOH C:2225 , HOH C:2226BINDING SITE FOR RESIDUE SO4 C1223
12BC3SOFTWAREALA C:167 , ARG D:149 , ASP D:150 , HOH D:2221 , HOH D:2222BINDING SITE FOR RESIDUE SO4 D1223
13BC4SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C1224
14BC5SOFTWAREPHE A:34 , GLU A:70 , HOH A:2110 , HOH A:2111 , HOH A:2113 , TYR C:78 , GLY C:151 , VAL C:184 , HOH C:2174 , HOH C:2227 , HOH C:2228BINDING SITE FOR RESIDUE SO4 C1225
15BC6SOFTWARECYS C:195 , GLU C:197 , TYR C:211BINDING SITE FOR RESIDUE SO3 C1226
16BC7SOFTWAREARG B:119 , ASN D:17 , HIS D:22 , HIS D:121 , HOH D:2223 , HOH D:2224 , HOH D:2225 , HOH D:2226BINDING SITE FOR RESIDUE SO4 D1224
17BC8SOFTWAREASP D:202 , LYS D:203BINDING SITE FOR RESIDUE SO4 D1225
18BC9SOFTWARELYS D:182 , GLY D:183 , HOH D:2176BINDING SITE FOR RESIDUE SO4 D1226
19CC1SOFTWARECYS D:195 , GLU D:197 , TYR D:211 , HOH D:2228BINDING SITE FOR RESIDUE SO3 D1227

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VVJ)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Leu A:220 -Pro A:221
4Gly B:48 -Pro B:49
5Phe B:83 -Pro B:84
6Leu B:220 -Pro B:221
7Gly C:48 -Pro C:49
8Phe C:83 -Pro C:84
9Leu C:220 -Pro C:221
10Gly D:48 -Pro D:49
11Phe D:83 -Pro D:84
12Leu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VVJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VVJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2VVJ)

(-) 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:219
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
         Q5S6Z9_LOBHE     2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
               SCOP domains d2vvja_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvj A   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAf--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
                                    11        21        31        41        51        61  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
                                                                                      61-NFA                                                                                                                                                             
                                                                                         64-IEY                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
         Q5S6Z9_LOBHE     2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d2vvjb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vvj B   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAf--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    11        21        31        41        51        61  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
                                                                                      61-NFA                                                                                                                                                              
                                                                                         64-IEY                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:222
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:224
                              1                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
         Q5S6Z9_LOBHE     - --MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
               SCOP domains d2vvjc_ C: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvj C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAf--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
                                     8        18        28        38        48        58  |  |  68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
                                                                                         61-NFA                                                                                                                                                             
                                                                                            64-IEY                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:221
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                             1                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
         Q5S6Z9_LOBHE     - -MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
               SCOP domains d2vvjd_ D: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -GFP-2vvjD01 D:1-219                                                                                                                                                                                                        --- Pfam domains (1)
           Pfam domains (2) -GFP-2vvjD02 D:1-219                                                                                                                                                                                                        --- Pfam domains (2)
           Pfam domains (3) -GFP-2vvjD03 D:1-219                                                                                                                                                                                                        --- Pfam domains (3)
           Pfam domains (4) -GFP-2vvjD04 D:1-219                                                                                                                                                                                                        --- Pfam domains (4)
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--.......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvj D   0 HMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAf--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
                                     9        19        29        39        49        59 |  |   69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
                                                                                        61-NFA                                                                                                                                                             
                                                                                           64-IEY
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VVJ)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5S6Z9_LOBHE | Q5S6Z9)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

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  Cis Peptide Bonds
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    Gly C:48 - Pro C:49   [ RasMol ]  
    Gly D:48 - Pro D:49   [ RasMol ]  
    Leu A:220 - Pro A:221   [ RasMol ]  
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  2vvj
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 Related Entries

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

UniProtKB/TrEMBL
        Q5S6Z9_LOBHE | Q5S6Z9: 1zux 2btj 2vvh 2vvi 3p8u 3s05 3tmr 3tmt 4ljb 4ljc 4ljd 4oy4 4r6b 5dtl 5fvf 5fvg 5fvi

(-) Related Entries Specified in the PDB File

1zux EOSFP FLUORESCENT PROTEIN- GREEN FORM
2btj FLUORESCENT PROTEIN EOSFP - RED FORM
2vvh IRISFP FLUORESCENT PROTEIN IN ITS GREEN FORM , CIS CONFORMATION
2vvi IRISFP FLUORESCENT PROTEIN IN ITS GREEN FORM , TRANS CONFORMATION