3QDC - JenaLib

Title :   CRYSTAL STRUCTURE OF NATRONOMONAS PHARAONIS SENSORY RHODOPSIN II IN THE ACTIVE STATE

Authors :   I. Gushchin, A. Reshetnyak, V. Borshchevskiy, A. Ishchenko, E. Round, S. Grudinin, M. Engelhard, G. Buldt, V. Gordeliy

Date :   18 Jan 11 (Deposition) - 14 Sep 11 (Release) - 28 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Phototaxis, Nphtrii, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Gushchin, A. Reshetnyak, V. Borshchevskiy, A. Ishchenko, E. Round S. Grudinin, M. Engelhard, G. Buldt, V. Gordeliy
Active State Of Sensory Rhodopsin Ii: Structural Determinants For Signal Transfer And Proton Pumping.
J. Mol. Biol. V. 412 591 2011
PubMed-ID: 21840321 | Reference-DOI: 10.1016/J.JMB.2011.07.022

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 33)

Sites (32, 32)

Asymmetric Unit (32, 32)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:76 , THR A:79 , THR A:80 , VAL A:108 , MET A:109 , GLY A:112 , PHE A:127 , PHE A:134 , TRP A:171 , TYR A:174 , PRO A:175 , ASP A:201 , THR A:204 , LYS A:205	BINDING SITE FOR RESIDUE RET A 240
02	AC2	SOFTWARE	GLY A:3 , VAL A:132 , GLY A:136 , TYR A:139 , PRO A:144 , THR A:191 , VAL A:192 , ALA A:195 , HOH A:291 , HOH A:301	BINDING SITE FOR RESIDUE BOG A 241
03	AC3	SOFTWARE	TYR A:36 , TYR A:37 , LEU A:40 , LEU A:90 , ILE A:156 , LEU A:159 , ALA A:212 , ALA A:216	BINDING SITE FOR RESIDUE LFA A 242
04	AC4	SOFTWARE	LEU A:110 , PHE A:113 , ALA A:114 , MET A:117 , LFA A:247	BINDING SITE FOR RESIDUE LFA A 243
05	AC5	SOFTWARE	L2P A:257 , LFA A:266 , LFA A:272	BINDING SITE FOR RESIDUE LFA A 244
06	AC6	SOFTWARE	THR A:106 , L2P A:257	BINDING SITE FOR RESIDUE LFA A 245
07	AC7	SOFTWARE	VAL A:138 , TYR A:139 , VAL A:142	BINDING SITE FOR RESIDUE LFA A 246
08	AC8	SOFTWARE	ALA A:114 , ILE A:169 , LFA A:243	BINDING SITE FOR RESIDUE LFA A 247
09	AC9	SOFTWARE	ARG A:35 , THR A:39 , LFA A:264	BINDING SITE FOR RESIDUE LFA A 248
10	BC1	SOFTWARE	LEU A:110 , ALA A:111 , ALA A:114 , LEU A:126 , MET A:129 , LFA A:251	BINDING SITE FOR RESIDUE LFA A 249
11	BC2	SOFTWARE	TRP A:24 , PHE A:210 , LEU A:213 , ASP A:214 , LFA A:267 , HOH A:307	BINDING SITE FOR RESIDUE LFA A 250
12	BC3	SOFTWARE	THR A:103 , THR A:106 , VAL A:107 , PHE A:176 , LEU A:180 , LEU A:187 , LFA A:249 , LFA A:271	BINDING SITE FOR RESIDUE LFA A 251
13	BC4	SOFTWARE	TRP A:9 , LEU A:16 , VAL A:52 , LFA A:258 , LFA A:261 , LFA A:266	BINDING SITE FOR RESIDUE LFA A 252
14	BC5	SOFTWARE	TRP A:9 , ALA A:55 , GLY A:57 , LFA A:261	BINDING SITE FOR RESIDUE LFA A 253
15	BC6	SOFTWARE	ILE A:121 , TYR A:124 , ALA A:125 , GLY A:128 , VAL A:132 , TYR A:199 , ILE A:211 , LFA A:255 , L2P A:260 , LFA A:261 , LFA A:262 , LFA A:268	BINDING SITE FOR RESIDUE LFA A 254
16	BC7	SOFTWARE	TRP A:24 , ILE A:121 , TYR A:199 , LEU A:202 , VAL A:203 , GLY A:207 , PHE A:210 , ASP A:214 , LFA A:254 , LFA A:267	BINDING SITE FOR RESIDUE LFA A 255
17	BC8	SOFTWARE	VAL A:49 , ALA A:50 , VAL A:58 , GLY A:59 , PRO A:71 , ILE A:74 , ASP A:75 , LEU A:78 , PHE A:113 , LFA A:244 , LFA A:245 , LFA A:258 , LFA A:264 , LFA A:272 , HOH A:332	BINDING SITE FOR RESIDUE L2P A 257
18	BC9	SOFTWARE	LEU A:16 , VAL A:49 , LFA A:252 , L2P A:257	BINDING SITE FOR RESIDUE LFA A 258
19	CC1	SOFTWARE	THR A:6 , TRP A:9 , LFA A:261	BINDING SITE FOR RESIDUE LFA A 259
20	CC2	SOFTWARE	ALA A:131 , PHE A:134 , PHE A:176 , LEU A:179 , LFA A:254 , LFA A:262	BINDING SITE FOR RESIDUE L2P A 260
21	CC3	SOFTWARE	TRP A:9 , ILE A:13 , LFA A:252 , LFA A:253 , LFA A:254 , LFA A:259	BINDING SITE FOR RESIDUE LFA A 261
22	CC4	SOFTWARE	LEU A:20 , LFA A:254 , L2P A:260	BINDING SITE FOR RESIDUE LFA A 262
23	CC5	SOFTWARE	ARG A:35 , PRO A:81 , LEU A:82 , TYR A:85 , LFA A:265	BINDING SITE FOR RESIDUE LFA A 263
24	CC6	SOFTWARE	ALA A:23 , GLY A:26 , VAL A:41 , GLY A:42 , LFA A:248 , L2P A:257	BINDING SITE FOR RESIDUE LFA A 264
25	CC7	SOFTWARE	LEU A:93 , ASP A:94 , SER A:95 , PHE A:98 , ILE A:102 , LFA A:263	BINDING SITE FOR RESIDUE LFA A 265
26	CC8	SOFTWARE	LEU A:56 , VAL A:58 , LFA A:244 , LFA A:252 , LFA A:272	BINDING SITE FOR RESIDUE LFA A 266
27	CC9	SOFTWARE	LEU A:7 , LEU A:10 , GLY A:14 , VAL A:132 , LEU A:135 , ALA A:195 , VAL A:198 , TYR A:199 , LEU A:202 , LFA A:250 , LFA A:255 , LFA A:268	BINDING SITE FOR RESIDUE LFA A 267
28	DC1	SOFTWARE	GLY A:3 , LEU A:7 , LEU A:10 , LFA A:254 , LFA A:267 , LFA A:269	BINDING SITE FOR RESIDUE LFA A 268
29	DC2	SOFTWARE	TYR A:139 , LFA A:268	BINDING SITE FOR RESIDUE LFA A 269
30	DC3	SOFTWARE	SER A:95 , ARG A:96	BINDING SITE FOR RESIDUE LFA A 270
31	DC4	SOFTWARE	PHE A:176 , LEU A:180 , VAL A:185 , LEU A:187 , LFA A:251	BINDING SITE FOR RESIDUE LFA A 271
32	DC5	SOFTWARE	VAL A:58 , LFA A:244 , L2P A:257 , LFA A:266	BINDING SITE FOR RESIDUE LFA A 272

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:219
 aligned with BACS2_NATPH | P42196 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
          BACS2_NATPH     1 MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATL 219
               SCOP domains d3qdca_ A: Sensory rhodopsin II                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BACTERIAL_OPS----------------------------------------------------------------------------------------------------------------BACTERIAL_OP----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qdc A   1 MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric/Biological 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.

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