3T45 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACTERIORHODOPSIN MUTANT A215T, A PHOTOTAXIS SIGNALING MUTANT AT 3.0 A RESOLUTION

Authors :   G. Ozorowski, H. Luecke

Date :   25 Jul 11 (Deposition) - 21 Dec 11 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.01

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Bacteriorhodopsins, Sensory Rhodopsin Ii, Microbial Rhodopsins, Lipids, Retinaldehyde, Schiff Bases, Light-Sensor, Phototaxis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. N. Spudich, G. Ozorowski, E. V. Schow, D. J. Tobias, J. L. Spudich, H. Luecke
A Transporter Converted Into A Sensor, A Phototaxis Signaling Mutant Of Bacteriorhodopsin At 3. 0 Angstrom.
J. Mol. Biol. V. 415 455 2012
PubMed-ID: 22123198 | Reference-DOI: 10.1016/J.JMB.2011.11.025

Molecule 1 - BACTERIORHODOPSIN (GROUND STATE)
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	HALOBACTERIUM SALINARUM
	Expression System Taxid	:	2242
	Expression System Vector Type	:	PLASMID
	Gene	:	BOP, VNG_1467G
	Mutation	:	YES
	Organism Scientific	:	HALOBACTERIUM SP. NRC-1
	Organism Taxid	:	64091
	Strain	:	ATCC 700922 / JCM 11081 / NRC-1
	Synonym	:	BR, BACTERIOOPSIN, BO

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 14)

No.	Name	Count	Type	Full Name
1	LI1	11	Ligand/Ion	1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2	RET	3	Ligand/Ion	RETINAL

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:86 , THR A:90 , LEU A:93 , MET A:118 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , LYS A:216	BINDING SITE FOR RESIDUE RET A 301
02	AC2	SOFTWARE	TRP B:86 , THR B:90 , LEU B:93 , MET B:118 , TRP B:138 , SER B:141 , THR B:142 , TRP B:182 , TYR B:185 , PRO B:186 , TRP B:189 , ASP B:212 , LYS B:216	BINDING SITE FOR RESIDUE RET B 301
03	AC3	SOFTWARE	TRP C:86 , THR C:90 , LEU C:93 , MET C:118 , TRP C:138 , SER C:141 , THR C:142 , TRP C:182 , TYR C:185 , PRO C:186 , TRP C:189 , ASP C:212 , LYS C:216	BINDING SITE FOR RESIDUE RET C 301
04	AC4	SOFTWARE	PHE A:135 , LEU A:190 , ALA A:196 , TRP B:12 , ILE B:203	BINDING SITE FOR RESIDUE LI1 A 600
05	AC5	SOFTWARE	TYR A:64 , GLY B:113 , GLY B:116 , ILE B:117	BINDING SITE FOR RESIDUE LI1 B 602
06	AC6	SOFTWARE	LEU A:15 , LEU B:25 , LEU B:58 , ALA C:139 , ILE C:140 , LI1 C:606	BINDING SITE FOR RESIDUE LI1 B 603
07	AC7	SOFTWARE	LI1 A:608 , TYR B:64 , TRP B:80 , PHE B:88 , LI1 B:615 , THR C:67 , TRP C:80 , ALA C:84 , GLY C:116 , GLY C:120 , LEU C:123 , LYS C:129	BINDING SITE FOR RESIDUE LI1 B 604
08	AC8	SOFTWARE	LEU B:28 , LYS B:40 , ALA B:44 , TYR C:147	BINDING SITE FOR RESIDUE LI1 B 605
09	AC9	SOFTWARE	TRP A:12 , GLY A:73 , GLN A:75 , ASN A:202 , ILE A:203 , LI1 B:603 , LEU C:190	BINDING SITE FOR RESIDUE LI1 C 606
10	BC1	SOFTWARE	TRP B:80 , LI1 B:604	BINDING SITE FOR RESIDUE LI1 B 615
11	BC2	SOFTWARE	TYR B:131 , LEU B:190 , LI1 B:612 , TRP C:12 , ASN C:202 , ILE C:203	BINDING SITE FOR RESIDUE LI1 B 611
12	BC3	SOFTWARE	LI1 B:611 , VAL C:199 , PRO C:200	BINDING SITE FOR RESIDUE LI1 B 612
13	BC4	SOFTWARE	ILE A:117 , TYR A:147 , LEU C:25 , LEU C:28 , GLY C:31 , PHE C:54	BINDING SITE FOR RESIDUE LI1 C 613
14	BC5	SOFTWARE	GLY A:116 , LEU A:127 , LI1 B:604 , MET C:56 , TYR C:64	BINDING SITE FOR RESIDUE LI1 A 608

(no "SS Bond" information available for 3T45)

(no "Cis Peptide Bond" information available for 3T45)

(no "SAP(SNP)/Variant" information available for 3T45)

Asymmetric/Biological Unit (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 B:82-94 C:82-94
2	BACTERIAL_OPSIN_RET	PS00327	Bacterial rhodopsins retinal binding site.	BACR_HALSA	221-232	3	A:208-219 B:208-219 C:208-219

(no "Exon" information available for 3T45)

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:225
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:225
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
           BACR_HALSA    20 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d3t45a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t45 A   7 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSTKVGFGLILLRSRAIFG 231
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:225
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
           BACR_HALSA    20 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d3t45b_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t45 B   7 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSTKVGFGLILLRSRAIFG 231
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

Chain C from PDB  Type:PROTEIN  Length:225
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:225
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
           BACR_HALSA    20 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d3t45c_ C: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t45 C   7 RPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSTKVGFGLILLRSRAIFG 231
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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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: automated matches (33)

Halobacterium sp. [TaxId: 64091] (6)

1a	d3t45a_	A:
1b	d3t45b_	B:
1c	d3t45c_	C:

(no "CATH Domain" information available for 3T45)

(no "Pfam Domain" information available for 3T45)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3t45)

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	3t45
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	BACR_HALSA \| P02945
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1c3w	BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION
1jgj	CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIGHTS INTO COLOR TUNING AND TRANSDUCER INTERACTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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Related Entries

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