2ZFE - JenaLib

Title :   CRYSTAL STRUCTURE OF BACTERIORHODOPSIN-XENON COMPLEX

Authors :   T. Kouyama

Date :   31 Dec 07 (Deposition) - 11 Nov 08 (Release) - 09 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Hydrophobic Cavity, Chromophore, Hydrogen Ion Transport, Ion Transport, Membrane, Photoreceptor Protein, Pyrrolidone Carboxylic Acid, Receptor, Retinal Protein, Sensory Transduction, Transmembrane, Transport, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Hayakawa, T. Kasahara, D. Hasegawa, K. Yoshimura, M. Murakami, T. Kouyama
Effect Of Xenon Binding To A Hydrophobic Cavity On The Proton Pumping Cycle In Bacteriorhodopsin
J. Mol. Biol. V. 384 812 2008
PubMed-ID: 18930734 | Reference-DOI: 10.1016/J.JMB.2008.09.075
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 10)

Asymmetric Unit (8, 10)

No.	Name	Count	Type	Full Name
1	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
2	L1P	3	Ligand/Ion	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
3	L2P	1	Ligand/Ion	2,3-DI-PHYTANYL-GLYCEROL
4	L3P	1	Ligand/Ion	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
5	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
6	RET	1	Ligand/Ion	RETINAL
7	SGA	1	Ligand/Ion	O3-SULFONYLGALACTOSE
8	XE	1	Ligand/Ion	XENON

Biological Unit 1 (7, 27)

No.	Name	Count	Type	Full Name
1	GLC	3	Ligand/Ion	ALPHA-D-GLUCOSE
2	L1P	9	Ligand/Ion	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
3	L2P	3	Ligand/Ion	2,3-DI-PHYTANYL-GLYCEROL
4	L3P	3	Ligand/Ion	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
5	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
6	RET	3	Ligand/Ion	RETINAL
7	SGA	3	Ligand/Ion	O3-SULFONYLGALACTOSE
8	XE	-1	Ligand/Ion	XENON

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:67 , LEU A:127 , HOH A:617 , HOH A:618	BINDING SITE FOR RESIDUE GLC A 400
02	AC2	SOFTWARE	TYR A:64 , LEU A:66 , THR A:67 , TRP A:80 , LYS A:129 , HOH A:617	BINDING SITE FOR RESIDUE MAN A 410
03	AC3	SOFTWARE	PRO A:70 , LYS A:129	BINDING SITE FOR RESIDUE SGA A 420
04	AC4	SOFTWARE	TRP A:86 , THR A:89 , THR A:90 , MET A:118 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , ASP A:212 , ALA A:215 , LYS A:216	BINDING SITE FOR RESIDUE RET A 250
05	AC5	SOFTWARE	THR A:24 , LEU A:28 , MET A:32 , SER A:35 , LYS A:40 , ALA A:44 , THR A:47 , LEU A:48 , ASP A:104 , THR A:107 , ALA A:110 , ILE A:117 , ILE A:140 , ALA A:143 , TYR A:147 , HOH A:620 , HOH A:634	BINDING SITE FOR RESIDUE L3P A 260
06	AC6	SOFTWARE	ILE A:52 , TYR A:64 , TRP A:80 , ALA A:84 , LEU A:87 , PHE A:88 , LEU A:109 , GLY A:113 , GLY A:116 , ILE A:117 , LEU A:123 , LEU A:127	BINDING SITE FOR RESIDUE L2P A 270
07	AC7	SOFTWARE	ARG A:7 , ALA A:14 , LEU A:62 , ILE A:140	BINDING SITE FOR RESIDUE L1P A 280
08	AC8	SOFTWARE	TYR A:131 , ILE A:198	BINDING SITE FOR RESIDUE L1P A 290
09	AC9	SOFTWARE	LEU A:22 , TYR A:26 , ALA A:143 , LEU A:146 , TYR A:150 , PHE A:154 , ARG A:225	BINDING SITE FOR RESIDUE L1P A 300
10	BC1	SOFTWARE	LEU A:95 , ILE A:108	BINDING SITE FOR RESIDUE XE A 638

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACR_HALSA	95-107	1	A:82-94
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR_HALSA	221-232	1	A:208-219

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BACTERIAL_OPSIN_1	PS00950	Bacterial rhodopsins signature 1.	BACR_HALSA	95-107	3	A:82-94
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR_HALSA	221-232	3	A:208-219

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:227
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       
           BACR_HALSA    18 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d2zfea_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 2zfeA00 A:5-231 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                           CATH domains
               Pfam domains -----Bac_rhodopsin-2zfeA01 A:10-231                                                                                                                                                                                                 Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfe A   5 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (BACR_HALSA | P02945)

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:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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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