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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIORHODOPSIN MUTANT L111A CRYSTALLIZED FROM BICELLES
 
Authors :  N. H. Joh, D. Yang, J. U. Bowie
Date :  02 May 09  (Deposition) - 22 Sep 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacteriorhodopsin, Packing Force, Van Der Waals, Evolutionary Constraint, Membrane Protein, Integral Membrane Protein, Helical Membrane Protein, Proton Transport, Cell Membrane, Chromophore, Hydrogen Ion Transport, Ion Transport, Membrane, Photoreceptor Protein, Pyrrolidone Carboxylic Acid, Receptor, Retinal Protein, Sensory Transduction, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. H. Joh, A. Oberai, D. Yang, J. P. Whitelegge, J. U. Bowie
Similar Energetic Contributions Of Packing In The Core Of Membrane And Water-Soluble Proteins.
J. Am. Chem. Soc. V. 131 10846 2009
PubMed-ID: 19603754  |  Reference-DOI: 10.1021/JA904711K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Chains: A
    Engineered: YES
    Expression System: HALOBACTERIUM SALINARUM
    Expression System Strain: L33
    Expression System Taxid: 2242
    Gene: BOP, VNG_1467G
    Mutation: YES
    Organism Common: HALOBACTERIUM HALOBIUM
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Synonym: BR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2D104Ligand/IonDECANE
3D128Ligand/IonDODECANE
4DD91Ligand/IonNONANE
5HP61Ligand/IonHEPTANE
6R161Ligand/IonHEXADECANE
7RET1Ligand/IonRETINAL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:86 , THR A:90 , 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:216BINDING SITE FOR RESIDUE RET A 301
02AC2SOFTWARED12 A:403BINDING SITE FOR RESIDUE D12 A 402
03AC3SOFTWARED12 A:402BINDING SITE FOR RESIDUE D12 A 403
04AC4SOFTWAREASN A:176BINDING SITE FOR RESIDUE D12 A 405
05AC5SOFTWARETHR A:17 , ALA A:44 , D12 A:251 , D12 A:256 , CPS A:501BINDING SITE FOR RESIDUE D10 A 406
06AC6SOFTWAREVAL A:136BINDING SITE FOR RESIDUE R16 A 411
07AC7SOFTWAREGLY A:6 , LYS A:41 , LEU A:61 , GLN A:105 , ILE A:108 , HOH A:298 , HOH A:329 , HOH A:351 , D10 A:406BINDING SITE FOR RESIDUE CPS A 501
08AC8SOFTWARELEU A:25BINDING SITE FOR RESIDUE D10 A 250
09AC9SOFTWARELEU A:15 , D10 A:406BINDING SITE FOR RESIDUE D12 A 251
10BC1SOFTWAREHOH A:375BINDING SITE FOR RESIDUE D12 A 254
11BC2SOFTWAREALA A:110BINDING SITE FOR RESIDUE D12 A 255
12BC3SOFTWARELEU A:28 , LEU A:48 , D10 A:406BINDING SITE FOR RESIDUE D12 A 256
13BC4SOFTWAREILE A:203BINDING SITE FOR RESIDUE D10 A 257

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BACTERIAL_OPSIN_1PS00950 Bacterial rhodopsins signature 1.BACR_HALSA95-107  1A:82-94
2BACTERIAL_OPSIN_RETPS00327 Bacterial rhodopsins retinal binding site.BACR_HALSA221-232  1A:208-219

(-) Exons   (0, 0)

(no "Exon" information available for 3HAP)

(-) Sequences/Alignments

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:226
 aligned with BACR_HALSA | P02945 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:226
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      
           BACR_HALSA    19 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 244
               SCOP domains d3hapa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 3hapA00 A:6-231 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------BACTERIAL_OPS-----------------------------------------------------------------------------------------------------------------BACTERIAL_OP------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hap A   6 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILAAVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
   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/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological 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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 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 1ixf 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 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

3han 3hao 3haq 3har 3has