3UE6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE DARK STRUCTURE OF THE BLUE-LIGHT PHOTORECEPTOR AUREOCHROME1 LOV

Authors :   D. Mitra, X. Yang, K. Moffat

Date :   28 Oct 11 (Deposition) - 11 Apr 12 (Release) - 20 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: A,B,C,D,E,F  (1x)

Keywords :   Pas/Lov Domain, Fmn-Binding Blue-Light Photoreceptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Mitra, X. Yang, K. Moffat
Crystal Structures Of Aureochrome1 Lov Suggest New Design Strategies For Optogenetics.
Structure V. 20 698 2012
PubMed-ID: 22483116 | Reference-DOI: 10.1016/J.STR.2012.02.016

Molecule 1 - AUREOCHROME1
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 176-337
	Gene	:	AUREO1
	Organism Scientific	:	VAUCHERIA FRIGIDA
	Organism Taxid	:	195983

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	FMN	6	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (2, 8)

No.	Name	Count	Type	Full Name
1	FMN	6	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:222 , ASN A:229 , ASN A:253 , CYS A:254 , ARG A:255 , LEU A:257 , GLN A:258 , VAL A:267 , ARG A:271 , ILE A:274 , LEU A:284 , ASN A:286 , ASN A:296 , PHE A:298 , TYR A:313 , GLY A:315 , GLN A:317 , HOH A:601	BINDING SITE FOR RESIDUE FMN A 500
2	AC2	SOFTWARE	VAL B:220 , THR B:222 , ASN B:229 , ASN B:253 , CYS B:254 , ARG B:255 , LEU B:257 , GLN B:258 , ILE B:270 , ARG B:271 , ILE B:274 , LEU B:284 , ASN B:286 , ASN B:296 , PHE B:298 , GLN B:317 , HOH B:501	BINDING SITE FOR RESIDUE FMN B 401
3	AC3	SOFTWARE	PRO B:227 , ASP B:228 , GLU E:261	BINDING SITE FOR RESIDUE PO4 B 402
4	AC4	SOFTWARE	THR C:222 , ASN C:229 , ASN C:253 , CYS C:254 , ARG C:255 , LEU C:257 , GLN C:258 , VAL C:267 , ARG C:271 , ILE C:274 , LEU C:284 , ASN C:286 , ASN C:296 , PHE C:298 , VAL C:300 , GLY C:315 , GLN C:317	BINDING SITE FOR RESIDUE FMN C 500
5	AC5	SOFTWARE	THR D:222 , ASN D:229 , ASN D:253 , CYS D:254 , ARG D:255 , LEU D:257 , GLN D:258 , VAL D:267 , ARG D:271 , ILE D:274 , LEU D:284 , ASN D:286 , ASN D:296 , PHE D:298 , VAL D:300 , GLY D:315 , GLN D:317	BINDING SITE FOR RESIDUE FMN D 500
6	AC6	SOFTWARE	THR E:222 , ASN E:229 , ASN E:253 , CYS E:254 , ARG E:255 , LEU E:257 , GLN E:258 , ILE E:270 , ARG E:271 , ILE E:274 , LEU E:284 , ASN E:286 , ASN E:296 , PHE E:298 , TYR E:313 , GLY E:315 , GLN E:317 , HOH E:602 , HOH E:605	BINDING SITE FOR RESIDUE FMN E 500
7	AC7	SOFTWARE	VAL F:220 , THR F:222 , ASN F:229 , ASN F:253 , CYS F:254 , ARG F:255 , LEU F:257 , GLN F:258 , VAL F:267 , ILE F:270 , ARG F:271 , ILE F:274 , LEU F:284 , ASN F:286 , ASN F:296 , PHE F:298 , VAL F:300 , TYR F:313 , GLY F:315 , GLN F:317 , HOH F:501	BINDING SITE FOR RESIDUE FMN F 401
8	AC8	SOFTWARE	TRP A:295 , GLU A:322 , ASP F:228	BINDING SITE FOR RESIDUE PO4 F 402

(no "SS Bond" information available for 3UE6)

Asymmetric Unit

No.	Residues
1	Gln D:216	-	Gln D:217
2	Arg E:199	-	Ile E:200
3	Glu E:202	-	Asp E:203

(no "SAP(SNP)/Variant" information available for 3UE6)

(no "PROSITE Motif" information available for 3UE6)

(no "Exon" information available for 3UE6)

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:135
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:135
                                   211       221       231       241       251       261       271       281       291       301       311       321       331     
         A8QW55_VAUFR   202 EDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEY 336
               SCOP domains d3ue6a_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eeeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ue6 A 202 EDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEY 336
                                   211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:128
                                   216       226       236       246       256       266       276       286       296       306       316       326        
         A8QW55_VAUFR   207 SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNI 334
               SCOP domains d3ue6b_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ue6 B 207 SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNI 334
                                   216       226       236       246       256       266       276       286       296       306       316       326

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:120
                                   225       235       245       255       265       275       285       295       305       315       325       335
         A8QW55_VAUFR   216 QQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIE 335
               SCOP domains d3ue6c_ C: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeee..eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ue6 C 216 QQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIE 335
                                   225       235       245       255       265       275       285       295       305       315       325       335

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:130
                                   215       225       235       245       255       265       275       285       295       305       315       325       335
         A8QW55_VAUFR   206 YSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIE 335
               SCOP domains d3ue6d_ D: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.....eeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeee..eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ue6 D 206 YSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIE 335
                                   215       225       235       245       255       265       275       285       295       305       315       325       335

Chain E from PDB  Type:PROTEIN  Length:138
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:138
                                   208       218       228       238       248       258       268       278       288       298       308       318       328        
         A8QW55_VAUFR   199 RILEDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEY 336
               SCOP domains d3ue6e_ E: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhh....eeeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ue6 E 199 RILEDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEY 336
                                   208       218       228       238       248       258       268       278       288       298       308       318       328

Chain F from PDB  Type:PROTEIN  Length:127
 aligned with A8QW55_VAUFR | A8QW55 from UniProtKB/TrEMBL  Length:348

    Alignment length:127
                                   217       227       237       247       257       267       277       287       297       307       317       327       
         A8QW55_VAUFR   208 LVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNI 334
               SCOP domains d3ue6f_ F: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.......eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeee..eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ue6 F 208 LVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNI 334
                                   217       227       237       247       257       267       277       287       297       307       317       327

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: Profilin-like (304)

Superfamily: PYP-like sensor domain (PAS domain) (163)

Family: automated matches (33)

Protein domain: automated matches (33)

Vaucheria frigida [TaxId: 195983] (2)

1a	d3ue6a_	A:
1b	d3ue6b_	B:
1c	d3ue6c_	C:
1d	d3ue6d_	D:
1e	d3ue6e_	E:
1f	d3ue6f_	F:

(no "CATH Domain" information available for 3UE6)

(no "Pfam Domain" information available for 3UE6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (A8QW55_VAUFR | A8QW55)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg E:199 - Ile E:200	[ RasMol ]
		Gln D:216 - Gln D:217	[ RasMol ]
		Glu E:202 - Asp E:203	[ RasMol ]

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	3ue6
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	A8QW55_VAUFR \| A8QW55
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	A8QW55_VAUFR \| A8QW55	:	3ulf

(no "Related Entries Specified in the PDB File" available for 3UE6)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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