1X0I - JenaLib

Title :   CRYSTAL STRUCTURE OF THE ACID BLUE FORM OF BACTERIORHODOPSIN

Authors :   H. Okumura, M. Murakami, T. Kouyama

Date :   23 Mar 05 (Deposition) - 02 Aug 05 (Release) - 09 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : 1  (2x)
Biol. Unit 1: 1  (3x)

Keywords :   7 Transmembrane Helices, Membrane Protein, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Okumura, M. Murakami, T. Kouyama
Crystal Structures Of Acid Blue And Alkaline Purple Forms O Bacteriorhodopsin
J. Mol. Biol. V. 351 481 2005
PubMed-ID: 16023672 | Reference-DOI: 10.1016/J.JMB.2005.06.026

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO 1:77 , ARG 1:82 , SER 1:193 , GLU 1:194 , LEU 1:201 , GLU 1:204 , HOH 1:607 , HOH 1:608 , HOH 1:609 , HOH 1:612	BINDING SITE FOR RESIDUE SO4 1 700
2	AC2	SOFTWARE	TRP 1:86 , TRP 1:138 , SER 1:141 , THR 1:142 , TRP 1:182 , TYR 1:185 , PRO 1:186 , ASP 1:212 , LYS 1:216	BINDING SITE FOR RESIDUE RET 1 250
3	AC3	SOFTWARE	LEU 1:25 , LYS 1:40 , ALA 1:44 , PHE 1:54 , THR 1:107 , ILE 1:117 , TYR 1:147 , HOH 1:635	BINDING SITE FOR RESIDUE L3P 1 260
4	AC4	SOFTWARE	THR 1:55 , MET 1:56 , PHE 1:88 , THR 1:121 , LEU 1:123 , VAL 1:124 , LEU 1:127	BINDING SITE FOR RESIDUE L2P 1 270
5	AC5	SOFTWARE	VAL 1:136 , ALA 1:139 , ILE 1:140	BINDING SITE FOR RESIDUE L3P 1 280
6	AC6	SOFTWARE	LEU 1:15	BINDING SITE FOR RESIDUE L3P 1 290

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	1:82-94
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR_HALSA	221-232	1	1:208-219

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.	BACR_HALSA	95-107	1	1:82-94
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR_HALSA	221-232	1	1:208-219

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain 1 from PDB  Type:PROTEIN  Length:215
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:226
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           BACR_HALSA    21 PEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEA 246
               SCOP domains d1x0i1_ 1: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 1x0i100 1:8-233 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                          CATH domains
               Pfam domains --Bac_rhodopsin-1x0i101 1:10-233                                                                                                                                                                                                   Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----------..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP-------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x0i 1   8 PEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYG-----------PIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEA 233
                                    17        27        37        47        57       | -        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      
                                                                                    65          77

Legend:		→ Mismatch	(orange background)
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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 1 (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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