2ZZL - JenaLib

Title :   STRUCTURE OF BACTERIORHODOPSIN'S M INTERMEDIATE AT PH 7

Authors :   M. Yamamoto, T. Kouyama

Date :   18 Feb 09 (Deposition) - 06 Oct 09 (Release) - 06 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Retinal, Protein-Lipid Complex, Reaction Intermediate, Cell Membrane, 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 :   M. Yamamoto, N. Hayakawa, M. Murakami, T. Kouyama
Crystal Structures Of Different Substates Of Bacteriorhodopsin'S M Intermediate At Various Ph Levels.
J. Mol. Biol. 2009
PubMed-ID: 19712684 | Reference-DOI: 10.1016/J.JMB.2009.08.047
(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	SOG	1	Ligand/Ion	2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL

Biological Unit 1 (8, 30)

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	SOG	3	Ligand/Ion	2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	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 , ASP A:212 , ALA A:215 , LYS A:216	BINDING SITE FOR RESIDUE RET A 250
02	AC2	SOFTWARE	GLY A:21 , LYS A:40 , ALA A:44 , LEU A:48 , ALA A:51 , ASP A:104 , THR A:107 , ILE A:117 , TYR A:147 , GLY A:155 , SER A:158 , HOH A:620	BINDING SITE FOR RESIDUE L3P A 260
03	AC3	SOFTWARE	THR A:55 , TYR A:64 , TRP A:80 , ALA A:84 , LEU A:87 , PHE A:88 , GLY A:116 , GLY A:120 , LEU A:127 , GLC A:400 , HOH A:628	BINDING SITE FOR RESIDUE L2P A 270
04	AC4	SOFTWARE	ARG A:7 , TRP A:10 , ALA A:14 , ALA A:18 , LEU A:61 , TYR A:133	BINDING SITE FOR RESIDUE L1P A 280
05	AC5	SOFTWARE	TYR A:131 , ILE A:198	BINDING SITE FOR RESIDUE L1P A 290
06	AC6	SOFTWARE	LEU A:22 , TYR A:26 , VAL A:29 , LYS A:30 , TYR A:150 , PHE A:154 , ARG A:225	BINDING SITE FOR RESIDUE L1P A 300
07	AC7	SOFTWARE	TYR A:64 , THR A:67 , LEU A:127 , L2P A:270 , MAN A:410 , HOH A:629 , HOH A:631 , HOH A:640	BINDING SITE FOR RESIDUE GLC A 400
08	AC8	SOFTWARE	TYR A:64 , LEU A:66 , THR A:67 , TRP A:80 , LYS A:129 , GLC A:400 , SGA A:420 , SOG A:430 , HOH A:630	BINDING SITE FOR RESIDUE MAN A 410
09	AC9	SOFTWARE	PRO A:70 , LYS A:129 , MAN A:410	BINDING SITE FOR RESIDUE SGA A 420
10	BC1	SOFTWARE	LEU A:62 , TYR A:64 , LEU A:127 , THR A:128 , LYS A:129 , TYR A:133 , MAN A:410 , HOH A:615 , HOH A:625	BINDING SITE FOR RESIDUE SOG A 430

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:228
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:228
                                    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 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 245
               SCOP domains d2zzla_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2zzlA00 A:5-232 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                            CATH domains
               Pfam domains -----Bac_rhodopsin-2zzlA01 A:10-232                                                                                                                                                                                                  Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zzl A   5 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 232
                                    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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