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(-) Description

Title :  CRYSTAL STRUCTURE OF LEUT WITH BOUND OG
 
Authors :  A. M. L. Winther, M. Quick, J. A. Javitch, P. Nissen
Date :  08 Mar 09  (Deposition) - 28 Apr 09  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transmembrane Transport, Neurotransmitter:Sodium Symport, Sodium-Coupled Transport, Nss, Aminoacid Transport, Symport, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Quick, A. M. L. Winther, L. Shi, P. Nissen, H. Weinstein, J. A. Javitch
Binding Of An Octylglucoside Detergent Molecule In The Second Substrate (S2) Site Of Leut Establishes An Inhibitor-Bound Conformation
Proc. Natl. Acad. Sci. Usa V. 106 5563 2009
PubMed-ID: 19307590  |  Reference-DOI: 10.1073/PNAS.0811322106
(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, AQ_2077
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5
    Synonym: LEUT

 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
1BOG6Ligand/IonB-OCTYLGLUCOSIDE
2CL1Ligand/IonCHLORIDE ION
3LEU1Mod. Amino AcidLEUCINE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1BOG6Ligand/IonB-OCTYLGLUCOSIDE
2CL-1Ligand/IonCHLORIDE ION
3LEU1Mod. Amino AcidLEUCINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1BOG12Ligand/IonB-OCTYLGLUCOSIDE
2CL-1Ligand/IonCHLORIDE ION
3LEU2Mod. Amino AcidLEUCINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:20 , VAL A:23 , ALA A:351 , THR A:354 , SER A:355BINDING SITE FOR RESIDUE NA A 516
02AC2SOFTWAREALA A:22 , ASN A:27 , THR A:254 , ASN A:286 , LEU A:519BINDING SITE FOR RESIDUE NA A 517
03AC3SOFTWARESER A:165BINDING SITE FOR RESIDUE CL A 518
04AC4SOFTWAREASN 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 , PHE A:259 , SER A:355 , NA A:517BINDING SITE FOR RESIDUE LEU A 519
05AC5SOFTWARELEU A:53 , ARG A:142 , GLU A:146 , PRO A:445 , ARG A:446 , TYR A:448 , HOH A:552 , HOH A:591BINDING SITE FOR RESIDUE BOG A 701
06AC6SOFTWARELEU A:166 , PHE A:167 , GLY A:439 , GLY A:440BINDING SITE FOR RESIDUE BOG A 702
07AC7SOFTWAREPRO A:164 , LEU A:166 , HIS A:391 , PHE A:395 , PHE A:488 , ILE A:491 , BOG A:704BINDING SITE FOR RESIDUE BOG A 703
08AC8SOFTWARELYS A:163 , HIS A:391 , PHE A:395 , LYS A:431 , PHE A:488 , BOG A:703 , BOG A:705BINDING SITE FOR RESIDUE BOG A 704
09AC9SOFTWAREILE A:161 , LYS A:431 , MET A:476 , GLU A:477 , GLU A:478 , THR A:479 , TRP A:481 , VAL A:483 , TRP A:484 , ARG A:487 , BOG A:704BINDING SITE FOR RESIDUE BOG A 705
10BC1SOFTWAREALA A:319 , LEU A:400BINDING SITE FOR RESIDUE BOG A 706

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GJD)

(-) Exons   (0, 0)

(no "Exon" information available for 3GJD)

(-) 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:510
 aligned with O67854_AQUAE | O67854 from UniProtKB/TrEMBL  Length:513

    Alignment length:512
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      513   
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504        |-  
         O67854_AQUAE     5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESA---   -
               SCOP domains d3gjda_ A: Na(+):neurotransmitter symporter homologue LeuT                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......--.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..eehhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gjd A   5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPP--TDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESAGTL 519
                                    14        24        34        44        54        64        74        84        94       104       114       124       | -|      144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514||
                                                                                                                                                         132  |                                                                                                                                                                                                                                                                                                                                                                                         515|
                                                                                                                                                            135                                                                                                                                                                                                                                                                                                                                                                                          519
   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 3GJD)

(-) Pfam Domains  (0, 0)

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

(-) 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 2qei 2qju 3f3a 3f3c 3f3d 3f3e 3f48 3f4i 3f4j 3gjc 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

3gjc