2F93 - JenaLib

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Title :   K INTERMEDIATE STRUCTURE OF SENSORY RHODOPSIN II/TRANSDUCER COMPLEX IN COMBINATION WITH THE GROUND STATE STRUCTURE

Authors :   R. I. Moukhametzianov, J. P. Klare, R. G. Efremov, C. Baecken, A. Goeppn J. Labahn, M. Engelhard, G. Bueldt, V. I. Gordeliy

Date :   05 Dec 05 (Deposition) - 07 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Menbrane Protein Complex, Signal Transduction, Photocycle State, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Moukhametzianov, J. P. Klare, R. Efremov, C. Baeken, A. Goppner, J. Labahn, M. Engelhard, G. Buldt, V. I. Gordeliy
Development Of The Signal In Sensory Rhodopsin And Its Transfer To The Cognate Transducer.
Nature V. 440 115 2006
PubMed-ID: 16452929 | Reference-DOI: 10.1038/NATURE04520
(for further references see the PDB file header)

Molecule 1 - SENSORY RHODOPSIN II
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET27BMOD
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SOP2, SOPII
	Organism Scientific	:	NATRONOMONAS PHARAONIS
	Organism Taxid	:	2257
	Synonym	:	SR-II

Molecule 2 - SENSORY RHODOPSIN II TRANSDUCER
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET27BMOD
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HTR2, HTRII
	Organism Scientific	:	NATRONOMONAS PHARAONIS
	Organism Taxid	:	2257
	Synonym	:	HTR-II, METHYL-ACCEPTING PHOTOTAXIS PROTEIN II, MPP-II

		1	2
Asymmetric Unit (2x)	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	RET	1	Ligand/Ion	RETINAL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	RET	1	Ligand/Ion	RETINAL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:36 , TYR A:37 , LEU A:40 , ARG A:152 , ILE A:156 , ALA A:212 , LEU A:213 , LEU A:219 , HOH A:329	BINDING SITE FOR RESIDUE BOG A 300
2	AC2	SOFTWARE	TRP A:76 , THR A:80 , VAL A:108 , GLY A:112 , PHE A:127 , PHE A:134 , TRP A:171 , TYR A:174 , TRP A:178 , ASP A:201 , THR A:204 , LYS A:205	BINDING SITE FOR RESIDUE RET A 301

(no "SS Bond" information available for 2F93)

(no "Cis Peptide Bond" information available for 2F93)

(no "SAP(SNP)/Variant" information available for 2F93)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACS2_NATPH	72-84	1	A:72-84
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACS2_NATPH	197-208	1	A:197-208

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACS2_NATPH	72-84	1	A:72-84
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACS2_NATPH	197-208	1	A:197-208

(no "Exon" information available for 2F93)

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:220
 aligned with BACS2_NATPH | P42196 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
          BACS2_NATPH     3 GLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAE 222
               SCOP domains d2f93a_ A: Sensory rhodopsin II                                                                                                                                                                                              SCOP domains
               CATH domains 2f93A00 A:3-222 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP-------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f93 A   3 GLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAE 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:51
 aligned with HTR2_NATPH | P42259 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:51
                                    38        48        58        68        78 
           HTR2_NATPH    29 VGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVA  79
               SCOP domains d2f93b1 B:29-79                                     SCOP domains
               CATH domains 2f93B00 B:29-79 Helix hairpin bin                   CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 2f93 B  29 VGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVA  79
                                    38        48        58        68        78

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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 '\|'

(no "Pfam Domain" information available for 2F93)

Asymmetric Unit(hide GO term definitions)

Chain A (BACS2_NATPH | P42196)

molecular function
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
biological process
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (HTR2_NATPH | P42259)

molecular function
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Biological Unit
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1h2s	GROUND STATE STRUCTURE OF SENSORY RHODOPSIN II AND ITS TRANSDUCER

Description

Compounds

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

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Exons (0, 0)

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