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(-) Description

Title :  CRYSTAL STRUCTURE OF MEOSFP IN ITS GREEN STATE
 
Authors :  V. Adam, G. U. Nienhaus, D. Bourgeois
Date :  15 Oct 10  (Deposition) - 19 Oct 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Beta-Barrel, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Adam, B. Moeyaert, C. C. David, H. Mizuno, M. Lelimousin, P. Dedecker, R. Ando, A. Miyawaki, J. Michiels, Y. Engelborghs, J. Hofkens
Rational Design Of Photoconvertible And Biphotochromic Fluorescent Proteins For Advanced Microscopy Applications.
Chem. Biol. V. 18 1241 2011
PubMed-ID: 22035793  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.08.007

(-) 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 Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: LOBOPHYLLIA HEMPRICHII
    Organism Taxid: 46758

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
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
3SO415Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1CR81Mod. 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
2SO32Ligand/IonSULFITE ION
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CR81Mod. 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
2SO31Ligand/IonSULFITE ION
3SO44Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CR81Mod. 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
2SO3-1Ligand/IonSULFITE ION
3SO43Ligand/IonSULFATE ION
Biological Unit 4 (3, 6)
No.NameCountTypeFull Name
1CR81Mod. 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
2SO31Ligand/IonSULFITE ION
3SO44Ligand/IonSULFATE ION
Biological Unit 5 (3, 23)
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
3SO415Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:195 , GLU A:197 , HOH A:2261 , PRO C:221BINDING SITE FOR RESIDUE SO3 A 1000
02AC2SOFTWARELYS A:182 , GLY A:183BINDING SITE FOR RESIDUE SO4 A 1010
03AC3SOFTWAREASN A:17 , HIS A:22 , HIS A:121 , ARG B:119 , HIS B:121 , HOH B:2278BINDING SITE FOR RESIDUE SO4 A 1020
04AC4SOFTWAREASP A:202 , LYS A:203BINDING SITE FOR RESIDUE SO4 A 1030
05AC5SOFTWAREVAL A:148 , ARG A:149 , ASP A:150 , HOH A:2045 , ALA C:167 , HOH C:2220BINDING SITE FOR RESIDUE SO4 A 1040
06AC6SOFTWAREPRO A:221 , HOH A:2113 , CYS C:195 , GLU C:197BINDING SITE FOR RESIDUE SO3 A 227
07AC7SOFTWARECYS B:195 , GLU B:197 , PRO D:221BINDING SITE FOR RESIDUE SO3 B 1000
08AC8SOFTWARELYS B:182 , GLY B:183BINDING SITE FOR RESIDUE SO4 B 1010
09AC9SOFTWAREARG A:119 , ASN B:17 , HIS B:22 , HIS B:121 , HOH B:2269BINDING SITE FOR RESIDUE SO4 B 1020
10BC1SOFTWAREASP B:202 , LYS B:203BINDING SITE FOR RESIDUE SO4 B 1030
11BC2SOFTWAREARG B:149 , ASP B:150 , ALA D:167BINDING SITE FOR RESIDUE SO4 B 1040
12BC3SOFTWAREASN C:17 , HIS C:22 , HIS C:121 , ARG D:119 , HOH D:2207BINDING SITE FOR RESIDUE SO4 C 1020
13BC4SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C 1030
14BC5SOFTWAREALA A:167 , HIS A:168 , VAL C:148 , ARG C:149 , ASP C:150 , PRO D:6BINDING SITE FOR RESIDUE SO4 C 1040
15BC6SOFTWAREPRO B:221 , CYS D:195 , GLU D:197 , TYR D:211 , HOH D:2025 , HOH D:2122BINDING SITE FOR RESIDUE SO3 D 1000
16BC7SOFTWARELYS D:182 , GLY D:183 , VAL D:184 , HOH D:2274BINDING SITE FOR RESIDUE SO4 D 1010
17BC8SOFTWAREARG C:104 , ARG C:119 , ASN D:17 , HIS D:22BINDING SITE FOR RESIDUE SO4 D 1020
18BC9SOFTWAREASP D:202 , LYS D:203BINDING SITE FOR RESIDUE SO4 D 1030
19CC1SOFTWAREALA B:167 , ARG D:149 , ASP D:150 , HOH D:2343BINDING SITE FOR RESIDUE SO4 D 1040

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P8U)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric 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 3P8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P8U)

(-) Exons   (0, 0)

(no "Exon" information available for 3P8U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:221
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    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 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3p8ua_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhh...--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p8u A   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIHMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    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                                                                                                                                                           


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 d3p8ub_ 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
                 3p8u B   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIHMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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 d3p8uc_ C: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--.............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p8u C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIHMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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:221
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    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 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3p8ud_ D: 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
                 3p8u D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIHMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P8U)

(-) Gene Ontology  (2, 2)

Asymmetric 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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  3p8u
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1zux WILD TYPE PROTEIN EOSFP IN ITS GREEN STATE
2btj WILD TYPE PROTEIN EOSFP IN ITS RED STATE
2vvh IRISFP, A PHOTOSWITCHABLE VARIANT OF EOSFP, IN ITS GREEN CIS CONFORMATION
2vvi IRISFP, A PHOTOSWITCHABLE VARIANT OF EOSFP, IN ITS GREEN TRANS CONFORMATION
2vvj IRISFP, A PHOTOSWITCHABLE VARIANT OF EOSFP, IN ITS RED CIS CONFORMATION