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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF LEUT COMPLEXED WITH L-ALANINE, SODIUM, AND CLOMIPRAMINE
 
Authors :  S. K. Singh, A. Yamashita, E. Gouaux
Date :  25 Jun 07  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Membrane Protein, Neurotransmitter Sodium Symporter, Occluded, Tricyclic Antidepressant, Inhibitor, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Singh, A. Yamashita, E. Gouaux
Antidepressant Binding Site In A Bacterial Homologue Of Neurotransmitter Transporters.
Nature V. 448 952 2007
PubMed-ID: 17687333  |  Reference-DOI: 10.1038/NATURE06038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SNF
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2BOG5Ligand/IonB-OCTYLGLUCOSIDE
3CXX2Ligand/Ion3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2BOG5Ligand/IonB-OCTYLGLUCOSIDE
3CXX2Ligand/Ion3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2BOG10Ligand/IonB-OCTYLGLUCOSIDE
3CXX4Ligand/Ion3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:142 , GLU A:146 , ARG A:446 , TYR A:448 , HOH A:836 , HOH A:892 , HOH A:893BINDING SITE FOR RESIDUE BOG A 701
02AC2SOFTWAREPHE A:167 , ILE A:170 , ARG A:438 , HOH A:860BINDING SITE FOR RESIDUE BOG A 702
03AC3SOFTWAREPRO A:164 , LEU A:166 , TYR A:169 , HIS A:391 , PHE A:395 , BOG A:704 , HOH A:876BINDING SITE FOR RESIDUE BOG A 703
04AC4SOFTWAREHIS A:391 , LEU A:392 , PHE A:488 , BOG A:703 , BOG A:705BINDING SITE FOR RESIDUE BOG A 704
05AC5SOFTWAREILE A:161 , LYS A:163 , LEU A:396 , THR A:479 , VAL A:483 , TRP A:484 , BOG A:704BINDING SITE FOR RESIDUE BOG A 705
06AC6SOFTWAREGLY A:20 , VAL A:23 , GLY A:24 , ALA A:351 , THR A:354 , SER A:355BINDING SITE FOR RESIDUE NA A 751
07AC7SOFTWAREALA A:22 , ASN A:27 , THR A:254 , ASN A:286 , ALA A:601BINDING SITE FOR RESIDUE NA A 752
08AC8SOFTWAREASN A:21 , ALA A:22 , GLY A:24 , LEU A:25 , GLY A:26 , ASN A:27 , TYR A:108 , PHE A:253 , THR A:254 , SER A:256 , NA A:752BINDING SITE FOR RESIDUE ALA A 601
09AC9SOFTWAREARG A:30 , GLN A:34 , PHE A:320 , ASP A:401 , ASP A:404BINDING SITE FOR RESIDUE CXX A 801
10BC1SOFTWARESER A:181 , ARG A:185 , GLY A:190 , ARG A:193 , PHE A:194 , PHE A:350BINDING SITE FOR RESIDUE CXX A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QEI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QEI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QEI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QEI)

(-) Exons   (0, 0)

(no "Exon" information available for 2QEI)

(-) 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:512
 aligned with O67854_AQUAE | O67854 from UniProtKB/TrEMBL  Length:513

    Alignment length:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       513    
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513    
         O67854_AQUAE     4 KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESA----   -
               SCOP domains d2qeia_ A: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------SNF-2qeiA01 A:167-508                                                                                                                                                                                                                                                                                                                                 --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------SNF-2qeiA02 A:167-508                                                                                                                                                                                                                                                                                                                                 --------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........--.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qei A   4 KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPP--TDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESAGTLA 601
                                    13        23        33        43        53        63        73        83        93       103       113       123        |- |     143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513  ||
                                                                                                                                                          132  |                                                                                                                                                                                                                                                                                                                                                                                          516|
                                                                                                                                                             135                                                                                                                                                                                                                                                                                                                                                                                           601
   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
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QEI)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SNF] (5)
(-)
Family: SNF (5)
(-)
Aquifex aeolicus (5)
1aSNF-2qeiA01A:167-508
1bSNF-2qeiA02A:167-508

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (O67854_AQUAE | O67854)
molecular function
    GO:0005328    neurotransmitter:sodium symporter activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neurotransmitter(out) + Na+(out) = neurotransmitter(in) + Na+(in).
    GO:0015293    symporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006836    neurotransmitter transport    The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0005887    integral component of plasma membrane    The component of the plasma 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O67854_AQUAE | O67854: 2a65 2q6h 2q72 2qb4 2qju 3f3a 3f3c 3f3d 3f3e 3f48 3f4i 3f4j 3gjc 3gjd 3gwu 3gwv 3gww 3mpn 3mpq 3qs4 3qs5 3qs6 3tt1 3tt3 3tu0 3usg 3usi 3usj 3usk 3usl 3usm 3uso 3usp 4fxz 4fy0 4hmk 4hod 4mm4 4mm5 4mm6 4mm7 4mm8 4mm9 4mma 4mmb 4mmc 4mmd 4mme 4mmf 5jae 5jaf 5jag

(-) Related Entries Specified in the PDB File

2a65 SAME PROTEIN COMPLEXED WITH L-LEUCINE AND SODIUM
2q6h SAME PROTEIN COMPLEXED WITH L-LEUCINE, SODIUM, AND CLOMIPRAMINE
2q72 SAME PROTEIN COMPLEXED WITH L-LEUCINE, SODIUM, AND IMIPRAMINE
2qb4 SAME PROTEIN COMPLEXED WITH L-LEUCINE, SODIUM, AND DESIPRAMINE