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Description

Title :   CRYSTAL STRUCTURE OF THE K INTERMEDIATE OF BACTERIORHODOPSIN

Authors :   Y. Matsui, K. Sakai, M. Murakami, Y. Shiro, S. Adachi, H. Okumura, T. Kouyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   20 Jun 02 (Deposition) - 18 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   7-Helices, 13-Cis Retinal, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Matsui, K. Sakai, M. Murakami, Y. Shiro, S. Adachi, H. Okumura, T. Kouyama
Specific Damage Induced By X-Ray Radiation And Structural Changes In The Primary Photoreaction Of Bacteriorhodopsin
J. Mol. Biol. V. 324 469 2002
PubMed-ID: 12445782 | Reference-DOI: 10.1016/S0022-2836(02)01110-5
(for further references see the PDB file header)

Compounds

Molecule 1 - BACTERIORHODOPSIN
	Chains	:	A
	Organism Scientific	:	HALOBACTERIUM SALINARUM
	Organism Taxid	:	2242
	Strain	:	JW3

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (6, 9)

Asymmetric Unit (6, 9)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	L2P	1	Ligand/Ion	2,3-DI-PHYTANYL-GLYCEROL
4	L3P	4	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

Biological Unit 1 (6, 27)

No.	Name	Count	Type	Full Name
1	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
2	GLC	3	Ligand/Ion	ALPHA-D-GLUCOSE
3	L2P	3	Ligand/Ion	2,3-DI-PHYTANYL-GLYCEROL
4	L3P	12	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

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:67 , LEU A:127 , L2P A:270 , MAN A:410 , HOH A:616 , HOH A:617	BINDING SITE FOR RESIDUE GLC A 400
2	AC2	SOFTWARE	TYR A:64 , LEU A:66 , THR A:67 , TRP A:80 , LYS A:129 , L2P A:270 , GLC A:400 , GAL A:420	BINDING SITE FOR RESIDUE MAN A 410
3	AC3	SOFTWARE	PRO A:70 , MAN A:410	BINDING SITE FOR RESIDUE GAL A 420
4	AC4	SOFTWARE	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 , ALA A:215 , LYS A:216	BINDING SITE FOR RESIDUE RET A 250
5	AC5	SOFTWARE	GLY A:21 , THR A:24 , VAL A:29 , SER A:35 , LYS A:40 , ALA A:44 , LEU A:48 , ALA A:51 , THR A:107 , ALA A:110 , ILE A:117 , ALA A:143 , TYR A:147 , HOH A:629 , HOH A:634	BINDING SITE FOR RESIDUE L3P A 260
6	AC6	SOFTWARE	MET A:56 , TYR A:64 , TRP A:80 , ALA A:84 , LEU A:87 , PHE A:88 , LEU A:92 , GLY A:116 , LEU A:127 , GLC A:400 , MAN A:410	BINDING SITE FOR RESIDUE L2P A 270
7	AC7	SOFTWARE	ARG A:7 , ALA A:14 , THR A:17 , ALA A:18 , LEU A:25 , TYR A:133 , VAL A:136 , ILE A:140	BINDING SITE FOR RESIDUE L3P A 280
8	AC8	SOFTWARE	LEU A:22 , TYR A:131 , ALA A:139 , LEU A:190 , ILE A:198 , L3P A:300	BINDING SITE FOR RESIDUE L3P A 290
9	AC9	SOFTWARE	LEU A:22 , TYR A:26 , VAL A:29 , LEU A:146 , TYR A:150 , PHE A:154 , ARG A:225 , L3P A:290	BINDING SITE FOR RESIDUE L3P A 300

SS Bonds (0, 0)

(no "SS Bond" information available for 1IXF)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1IXF)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1IXF)

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)

(no "Exon" information available for 1IXF)

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 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 d1ixfa_ A: Bacteriorhodopsin                                                                                                                                                                                                        SCOP domains
               CATH domains 1ixfA00 A:5-231 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixf 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

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)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Family A G protein-coupled receptor-like (138)

Superfamily: Family A G protein-coupled receptor-like (138)

Family: Bacteriorhodopsin-like (107)

Protein domain: Bacteriorhodopsin (61)

Halobacterium salinarum [TaxId: 2242] (58)

d1ixfa_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Rhopdopsin 7-helix transmembrane proteins (128)

Homologous Superfamily: Rhopdopsin 7-helix transmembrane proteins (128)

Halobacterium salinarum. Organism_taxid: 2242. Strain: jw3 (9)

1ixfA00

A:5-231

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1IXF)

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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	1ixf
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	BACR_HALSA \| P02945	:	1ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1qm8 1r2n 1r84 1s51 1s52 1s53 1s54 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4md2 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9

Related Entries Specified in the PDB File

1iw6	1IW6 CONTAINS THE GROUND STATE OF BACTERIOHRHODOPSIN
1iw9	1IW9 CONTAINS THE M INTERMEDIATE OF BACTERIORHODOPSIN RELATED ID: MY_001000028.2 RELATED DB: TARGETDB