3E5W - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF FP611

Authors :   K. Nienhaus, H. Nar, R. Heilker, J. Wiedenmann, G. U. Nienhaus

Date :   14 Aug 08 (Deposition) - 23 Sep 08 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.71

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)

Keywords :   Chromophore, Luminescence, Photoprotein, Rfp639, Eqfp611, Cis Trans Isomer, Red Fluorescent Protein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Nienhaus, H. Nar, R. Heilker, J. Wiedenmann, G. U. Nienhaus
Trans-Cis Isomerization Is Responsible For The Red-Shifted Fluorescence In Variants Of The Red Fluorescent Protein Eqfp611.
J. Am. Chem. Soc. V. 130 12578 2008
PubMed-ID: 18761441 | Reference-DOI: 10.1021/JA8046443

Molecule 1 - RED FLUORESCENT PROTEIN EQFP611
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15PREP4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SEA ANEMONE
	Organism Scientific	:	ENTACMAEA QUADRICOLOR
	Organism Taxid	:	6118
	Other Details	:	SYNONYMOUS SOURCE ORGANISM NAME PARASICYONIS ACTINOSTOLOIDES
	Synonym	:	GFP-LIKE CHROMOPROTEIN; FP611

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NRQ	4	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NRQ	2	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NRQ	2	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(no "Site" information available for 3E5W)

(no "SS Bond" information available for 3E5W)

Asymmetric Unit

No.	Residues
1	Gly A:49	-	Pro A:50
2	Phe A:84	-	Pro A:85
3	Gly B:49	-	Pro B:50
4	Phe B:84	-	Pro B:85
5	Gly C:49	-	Pro C:50
6	Phe C:84	-	Pro C:85
7	Gly D:49	-	Pro D:50
8	Phe D:84	-	Pro D:85

(no "SAP(SNP)/Variant" information available for 3E5W)

(no "PROSITE Motif" information available for 3E5W)

(no "Exon" information available for 3E5W)

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:227
 aligned with RFP_ENTQU | Q8ISF8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
            RFP_ENTQU     3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFMYGSKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPNTEMLYPADGGLRGYSQMALNVDGGGYLSCSFETTYRSKKTVENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
               SCOP domains d3e5wa_ 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............eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5w A   3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFm--SKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPSTEMLYPADGGLRGYCQMALNVDGGGYLFCSFETTYRSKKTDENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
                                    12        22        32        42        52        62|  |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
                                                                                       63-NRQ

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with RFP_ENTQU | Q8ISF8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
            RFP_ENTQU     3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFMYGSKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPNTEMLYPADGGLRGYSQMALNVDGGGYLSCSFETTYRSKKTVENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
               SCOP domains d3e5wb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5w B   3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFm--SKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPSTEMLYPADGGLRGYCQMALNVDGGGYLFCSFETTYRSKKTDENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
                                    12        22        32        42        52        62|  |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
                                                                                       63-NRQ

Chain C from PDB  Type:PROTEIN  Length:227
 aligned with RFP_ENTQU | Q8ISF8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
            RFP_ENTQU     3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFMYGSKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPNTEMLYPADGGLRGYSQMALNVDGGGYLSCSFETTYRSKKTVENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
               SCOP domains d3e5wc_ 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...eeeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5w C   3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFm--SKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPSTEMLYPADGGLRGYCQMALNVDGGGYLFCSFETTYRSKKTDENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
                                    12        22        32        42        52        62|  |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
                                                                                       63-NRQ

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with RFP_ENTQU | Q8ISF8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
            RFP_ENTQU     3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFMYGSKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPNTEMLYPADGGLRGYSQMALNVDGGGYLSCSFETTYRSKKTVENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
               SCOP domains d3e5wd_ D: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5w D   3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFm--SKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPSTEMLYPADGGLRGYCQMALNVDGGGYLFCSFETTYRSKKTDENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKFCDLPSKLGRL 231
                                    12        22        32        42        52        62|  |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
                                                                                       63-NRQ

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 '\|'

Asymmetric 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: Fluorescent proteins (271)

Protein domain: automated matches (102)

Sea anemone (Entacmaea quadricolor) [TaxId: 6118] (21)

1a	d3e5wa_	A:
1b	d3e5wb_	B:
1c	d3e5wc_	C:
1d	d3e5wd_	D:

(no "CATH Domain" information available for 3E5W)

(no "Pfam Domain" information available for 3E5W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RFP_ENTQU | Q8ISF8)

biological process
	GO:0008218		bioluminescence		The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0018298		protein-chromophore linkage		The covalent or noncovalent attachment of a chromophore to a protein.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		NRQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3e5w)

	Cis Peptide Bonds
		Gly A:49 - Pro A:50	[ RasMol ]
		Gly B:49 - Pro B:50	[ RasMol ]
		Gly C:49 - Pro C:50	[ RasMol ]
		Gly D:49 - Pro D:50	[ RasMol ]
		Phe A:84 - Pro A:85	[ RasMol ]
		Phe B:84 - Pro B:85	[ RasMol ]
		Phe C:84 - Pro C:85	[ RasMol ]
		Phe D:84 - Pro D:85	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3e5w
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		Orientation in Membranes	:	OPM
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	RFP_ENTQU \| Q8ISF8	:	1uis 3e5t 3e5v 3ip2 3u0l 3u0m 3u0n

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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