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(-) Description

Title :  IRISFP FLUORESCENT PROTEIN IN ITS GREEN FORM, TRANS 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) - 11 Nov 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  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2SO34Ligand/IonSULFITE ION
3SO416Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:17 , HIS A:22 , HIS A:121 , HOH A:2291 , HOH A:2292 , ARG C:104 , ARG C:119BINDING SITE FOR RESIDUE SO4 A1222
02AC2SOFTWAREASP B:150 , HOH B:2198 , HOH B:2199 , HOH B:2200BINDING SITE FOR RESIDUE SO4 B1224
03AC3SOFTWAREASP A:202 , LYS A:203 , HOH A:2277BINDING SITE FOR RESIDUE SO4 A1223
04AC4SOFTWARELYS A:182 , GLY A:183BINDING SITE FOR RESIDUE SO4 A1224
05AC5SOFTWARECYS A:195 , ILE A:196 , GLU A:197 , TYR A:211 , HIS A:213BINDING SITE FOR RESIDUE SO3 A1225
06AC6SOFTWAREHIS A:74 , HIS A:217 , SER A:218 , HOH A:2293 , HOH A:2294BINDING SITE FOR RESIDUE SO4 A1226
07AC7SOFTWAREASN B:17 , HIS B:22 , HOH B:2201 , HOH B:2202 , HOH B:2203BINDING SITE FOR RESIDUE SO4 B1225
08AC8SOFTWAREASP A:150 , HOH A:2212 , HOH A:2296 , HOH A:2297 , ALA B:167BINDING SITE FOR RESIDUE SO4 A1227
09AC9SOFTWAREASP B:202 , LYS B:203 , HOH B:2181BINDING SITE FOR RESIDUE SO4 B1226
10BC1SOFTWARELYS B:182 , GLY B:183 , HOH B:2204BINDING SITE FOR RESIDUE SO4 B1227
11BC2SOFTWAREPRO A:221 , CYS B:195 , GLU B:197 , TYR B:211 , HOH B:2205BINDING SITE FOR RESIDUE SO3 B1228
12BC3SOFTWAREARG A:119 , ASN C:17 , HIS C:22 , HIS C:121 , HOH C:2257 , HOH C:2258BINDING SITE FOR RESIDUE SO4 C1224
13BC4SOFTWAREALA C:167 , VAL D:148 , ARG D:149 , ASP D:150 , HOH D:2234 , HOH D:2235BINDING SITE FOR RESIDUE SO4 D1223
14BC5SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C1225
15BC6SOFTWAREPHE A:34 , GLU A:70 , HOH A:2063 , HOH A:2128 , TYR C:78 , GLY C:151 , LEU C:186 , HOH C:2260 , HOH C:2261 , HOH C:2262 , HOH C:2263BINDING SITE FOR RESIDUE SO4 C1226
16BC7SOFTWARECYS C:195 , ILE C:196 , GLU C:197 , TYR C:211 , GLU C:212 , HIS C:213 , HOH C:2264BINDING SITE FOR RESIDUE SO3 C1227
17BC8SOFTWAREARG B:119 , HOH B:2101 , ASN D:17 , HIS D:22 , HIS D:121 , HOH D:2237BINDING SITE FOR RESIDUE SO4 D1224
18BC9SOFTWAREASP D:202 , LYS D:203BINDING SITE FOR RESIDUE SO4 D1225
19CC1SOFTWARELYS D:182 , GLY D:183 , HOH D:2238BINDING SITE FOR RESIDUE SO4 D1226
20CC2SOFTWARECYS D:195 , ILE D:196 , GLU D:197 , TYR D:211 , HIS D:213 , HOH D:2240BINDING SITE FOR RESIDUE SO3 D1227

(-) SS Bonds  (0, 0)

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

(-) 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 2VVI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VVI)

(-) 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:218
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:220
                                    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 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLP 221
               SCOP domains d2vvia_ 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
                 2vvi A   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLP 221
                                    11        21        31        41        51        61  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
                                                                                      61  |                                                                                                                                                             
                                                                                         64-CR8                                                                                                                                                         


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 d2vvib_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh...--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vvi 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  |                                                                                                                                                               
                                                                                         64-CR8                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:223
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:225
                              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     - --MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d2vvic_ C: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhh....--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvi C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  |  |  68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     
                                                                                         61  |                                                                                                                                                               
                                                                                            64-CR8                                                                                                                                                           


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

    Alignment length:222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
         Q5S6Z9_LOBHE     1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
               SCOP domains d2vvid_ D: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhh...--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vvi D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPD 222
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
                                                                                       61  |                                                                                                                                                              
                                                                                          64-CR8
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VVI)

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q5S6Z9_LOBHE | Q5S6Z9: 1zux 2btj 2vvh 2vvj 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
2vvj IRISFP FLUORESCENT PROTEIN IN ITS RED FORM, CIS CONFORMATION