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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF A PHOTOBLEACHED STATE OF IRISFP UNDER LOW INTENSITY LASER-LIGHT

Authors :   C. Duan, V. Adam, M. Byrdin, J. Ridard, S. Kieffer-Jacquinod, C. Morlot D. Arcizet, I. Demachy, D. Bourgeois

Date :   04 Jul 13 (Deposition) - 09 Oct 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Fluorescent Protein, Photobleaching, Beta-Barrel, Oxidation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Duan, V. Adam, M. Byrdin, J. Ridard, S. Kieffer-Jaquinod, C. Morlot D. Arcizet, I. Demachy, D. Bourgeois
Structural Evidence For A Two-Regime Photobleaching Mechanism In A Reversibly Switchable Fluorescent Protein.
J. Am. Chem. Soc. V. 135 15841 2013
PubMed-ID: 24059326 | Reference-DOI: 10.1021/JA406860E

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
	Chains	:	A, B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	LOBED BRAIN CORAL
	Organism Scientific	:	LOBOPHYLLIA HEMPRICHII
	Organism Taxid	:	46758

Molecule 2 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	LOBED BRAIN CORAL
	Organism Scientific	:	LOBOPHYLLIA HEMPRICHII
	Organism Taxid	:	46758

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 31)

No.	Name	Count	Type	Full Name
1	CR8	4	Mod. Amino Acid	2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2	CSX	4	Mod. Amino Acid	S-OXY CYSTEINE
3	MHO	3	Mod. Amino Acid	S-OXYMETHIONINE
4	SO3	4	Ligand/Ion	SULFITE ION
5	SO4	16	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:17 , HIS A:22 , HOH A:472 , HOH A:498 , ARG C:119	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	ASP A:202 , LYS A:203	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	LYS A:182 , GLY A:183 , HOH A:480	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	CYS A:195 , GLU A:197 , TYR A:211 , HOH A:426 , HOH A:490 , HOH A:509 , PRO B:221	BINDING SITE FOR RESIDUE SO3 A 304
05	AC5	SOFTWARE	VAL A:148 , ARG A:149 , ASP A:150 , HOH A:473 , ALA B:167 , HOH B:473	BINDING SITE FOR RESIDUE SO4 A 305
06	AC6	SOFTWARE	ALA A:167 , ARG B:149 , ASP B:150 , HOH B:406 , HOH B:414	BINDING SITE FOR RESIDUE SO4 B 301
07	AC7	SOFTWARE	ASN B:17 , HIS B:22 , HIS B:121 , HOH B:431	BINDING SITE FOR RESIDUE SO4 B 302
08	AC8	SOFTWARE	ASP B:202 , LYS B:203 , HOH B:445	BINDING SITE FOR RESIDUE SO4 B 303
09	AC9	SOFTWARE	LYS B:182 , GLY B:183	BINDING SITE FOR RESIDUE SO4 B 304
10	BC1	SOFTWARE	PRO A:221 , GLU B:197 , TYR B:211 , HOH B:478	BINDING SITE FOR RESIDUE SO3 B 305
11	BC2	SOFTWARE	ARG A:119 , HOH A:440 , ASN C:17 , HIS C:22 , HIS C:121 , HOH C:417 , HOH C:496 , HOH C:500	BINDING SITE FOR RESIDUE SO4 C 301
12	BC3	SOFTWARE	ASP C:202 , LYS C:203 , HOH C:459 , HOH C:468	BINDING SITE FOR RESIDUE SO4 C 302
13	BC4	SOFTWARE	GLU A:70 , TYR C:78 , VAL C:184 , LEU C:186 , HOH C:449 , HOH C:456 , HOH C:457	BINDING SITE FOR RESIDUE SO4 C 303
14	BC5	SOFTWARE	GLU C:46 , GLY C:47	BINDING SITE FOR RESIDUE SO4 C 304
15	BC6	SOFTWARE	CYS C:195 , TYR C:211 , HIS C:213 , PRO D:221	BINDING SITE FOR RESIDUE SO3 C 305
16	BC7	SOFTWARE	ASN C:166 , ALA C:167 , ARG D:149 , ASP D:150	BINDING SITE FOR RESIDUE SO4 D 301
17	BC8	SOFTWARE	ASN D:17 , HIS D:22 , HIS D:121 , HOH D:469	BINDING SITE FOR RESIDUE SO4 D 302
18	BC9	SOFTWARE	ASP D:202 , LYS D:203 , HOH D:461	BINDING SITE FOR RESIDUE SO4 D 303
19	CC1	SOFTWARE	LYS D:182 , GLY D:183	BINDING SITE FOR RESIDUE SO4 D 304
20	CC2	SOFTWARE	PRO C:221 , CYS D:195 , GLU D:197 , TYR D:211 , HOH D:456	BINDING SITE FOR RESIDUE SO3 D 305

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

Asymmetric/Biological Unit

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

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

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

(no "Exon" information available for 4LJD)

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:221
                                                                                                                                                                                                                                                             
               SCOP domains d4ljda_ 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..........eeeee.eeeeee.....eeeeeee.eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljd A   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITmALLLEGNAHYRcDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152      |162       172       182       192       202       212       222 
                                                                                       61|                                                                                            159-MHO     171-CSX                                                
                                                                                        64-CR8

Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d4ljdb_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.......hhhhhh.................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljd B   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITmALLLEGNAHYRcDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    11        21        31        41        51        61|       73        83        93       103       113       123       133       143       153     | 163       173       183       193       203       213       223
                                                                                      61|                                                                                            159-MHO     171-CSX                                                
                                                                                       64-CR8

Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains d4ljdc_ 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
                 4ljd C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRcDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  ||    70        80        90       100       110       120       130       140       150       160       170|      180       190       200       210       220   
                                                                                         61|                                                                                                        171-CSX                                                
                                                                                          64-CR8

Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains d4ljdd_ D: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.......hhhhhh.................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..........eeeee.eeeeee.....eeeeeee.eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljd D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITmALLLEGNAHYRcDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152      |162       172       182       192       202       212       222 
                                                                                       61|                                                                                            159-MHO     171-CSX                                                
                                                                                        64-CR8

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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: GFP-like (339)

Superfamily: GFP-like (339)

Family: automated matches (66)

Protein domain: automated matches (66)

Lobophyllia hemprichii [TaxId: 46758] (12)

1a	d4ljda_	A:
1b	d4ljdb_	B:
1c	d4ljdc_	C:
1d	d4ljdd_	D:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ RasMol ]
		Gly B:48 - Pro B:49	[ RasMol ]
		Gly C:48 - Pro C:49	[ RasMol ]
		Gly D:48 - Pro D:49	[ RasMol ]
		Leu A:220 - Pro A:221	[ RasMol ]
		Leu B:220 - Pro B:221	[ RasMol ]
		Leu C:220 - Pro C:221	[ RasMol ]
		Leu D:220 - Pro D:221	[ RasMol ]
		Phe A:83 - Pro A:84	[ RasMol ]
		Phe B:83 - Pro B:84	[ RasMol ]
		Phe C:83 - Pro C:84	[ RasMol ]
		Phe D:83 - Pro D:84	[ RasMol ]

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	4ljd
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2vvh	CRYSTAL STRUCTURE OF IRISFP IN ITS GREEN STATE (CHROMOPHORE IN CIS CONFORMATION)
2vvi	CRYSTAL STRUCTURE OF IRISFP IN ITS DARK STATE (CHROMOPHORE IN TRANS CONFORMATION)
2vvj	CRYSTAL STRUCTURE OF IRISFP IN ITS RED STATE(CHROMOPHORE IN CIS CONFORMATION)
3tmr	CRYSTAL STRUCTURE OF NATIVE IRISFP (LOW X-RAY DOSE, PLANAR CHROMOPHORE)
3tmt	CRYSTAL STRUCTURE OF IRISFP IN ITS BLINKED STATE (DISTORTED CHROMOPHORE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 31)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

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Gene Ontology (2, 2)

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