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(-) Description

Title :  CRYSTAL STRUCTURE OF MATE IN COMPLEX WITH MAD3S
 
Authors :  Y. Tanaka, R. Ishitani, O. Nureki
Date :  27 Jul 12  (Deposition) - 03 Apr 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mate, Multidrug Transporter, Macrocyclic Peptide, Transport Protein, Transport Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tanaka, C. J. Hipolito, A. D. Maturana, K. Ito, T. Kuroda, T. Higuchi T. Katoh, H. E. Kato, M. Hattori, K. Kumazaki, T. Tsukazaki, R. Ishitani, H. Suga, O. Nureki
Structural Basis For The Drug Extrusion Mechanism By A Mate Multidrug Transporter.
Nature V. 496 247 2013
PubMed-ID: 23535598  |  Reference-DOI: 10.1038/NATURE12014

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF0708
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: JCM 8422
    Synonym: ARCHAEAL-TYPE TRANSPORTER
 
Molecule 2 - MACROCYCLIC PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: SELECTED BY THE RAPID SYSTEM PROTOCOL
    Synonym: MAD3S
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DPN1Mod. Amino AcidD-PHENYLALANINE
3OLC12Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:61 , GLY A:65 , OLC A:506BINDING SITE FOR RESIDUE OLC A 501
02AC2SOFTWAREILE A:106 , THR A:190 , PRO A:234BINDING SITE FOR RESIDUE OLC A 502
03AC3SOFTWARELEU A:101 , PHE A:148 , ARG A:221 , THR A:228 , LEU A:229BINDING SITE FOR RESIDUE OLC A 503
04AC4SOFTWAREVAL A:33 , LEU A:105 , LEU A:116 , ARG A:141 , ALA A:145 , MET A:170 , VAL A:174 , ILE A:181BINDING SITE FOR RESIDUE OLC A 504
05AC5SOFTWARELEU A:36 , ALA A:145 , TYR A:200BINDING SITE FOR RESIDUE OLC A 505
06AC6SOFTWAREGLY A:65 , ALA A:68 , SER A:250 , LEU A:254 , SER A:257 , OLC A:501BINDING SITE FOR RESIDUE OLC A 506
07AC7SOFTWAREILE A:29 , TYR A:200BINDING SITE FOR RESIDUE OLC A 507
08AC8SOFTWAREILE A:113 , THR A:114 , LEU A:179BINDING SITE FOR RESIDUE OLC A 508
09AC9SOFTWAREPRO A:117 , ARG A:168 , TYR A:215 , TRP A:216 , LYS A:220 , ASP A:222BINDING SITE FOR RESIDUE OLC A 509
10BC1SOFTWARELYS A:4 , THR A:6 , GLY A:8 , GLY A:164 , ASP A:165 , ALA A:166 , ASN A:167 , ASP A:222 , THR A:223 , TYR A:224BINDING SITE FOR RESIDUE OLC A 510
11BC2SOFTWAREGLU A:393BINDING SITE FOR RESIDUE OLC A 512
12BC3SOFTWAREGLN A:34 , TYR A:37 , ASN A:38 , PHE A:60 , PHE A:63 , MET A:64 , ILE A:67 , ALA A:71 , ILE A:150 , ASN A:153 , ASN A:154 , ASN A:157 , MET A:173 , MET A:206 , THR A:209 , GLN A:253 , MET A:256 , THR A:280BINDING SITE FOR CHAIN B OF MACROCYCLIC PEPTIDE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Lys A:4 -Thr A:5
2Gly A:130 -Glu A:131
3Arg A:230 -Asp A:231
4Ala A:270 -Gly A:271
5Cys B:7 -Leu B:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VVS)

(-) 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:444
 aligned with Q8U2X0_PYRFU | Q8U2X0 from UniProtKB/TrEMBL  Length:461

    Alignment length:451
                                    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 
         Q8U2X0_PYRFU     4 KTTKGVQLLRGDPKKAIVRLSIPMMIGMSVQTLYNLADGIWVSGLGPESLAAVGLFFPVFMGIIALAAGLGVGTSSAIARRIGARDKEGADNVAVHSLILSLILGVTITITMLPAIDSLFRSMGAKGEAVELAIEYARVLLAGAFIIVFNNVGNGILRGEGDANRAMLAMVLGSGLNIVLDPIFIYTLGFGVVGAAYATLLSMVVTSLFIAYWLFVKRDTYVDITLRDFSPSREILKDILRVGLPSSLSQLSMSIAMFFLNSVAITAGGENGVAVFTSAWRITMLGIVPILGMAAATTSVTGAAYGERNVEKLETAYLYAIKIAFMIELAVVAFIMLFAPQVAYLFTYSESAQVIKGDLISALRTLPVFLVLTPFGMMTSAMFQGIGEGEKSLILTIFRTLVMQVGFAYIFVHYTTLGLRGVWIGIVIGNMVAAIVGFLWGRMRISALKKT 454
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vvs A   4 KTTKGVQLLRGDPKKAIVRLSIPMMIGMSVQTLYNLADGIWVSGLGPESLAAVGLFFPVFMGIIALAAGLGVGTSSAIARRIGARDKEGADNVAVHSLILSLILGVTITITMLPAIDSLFRSMGAKGEAVELAIEYARVLLAGAFIIVFNNVGNGILRGEGDANRAMLAMVLGSGLNIVLDPIFIYTLGFGVVGAAYATLLSMVVTSLFIAYWLFVKRDTYVDITLRDFSPSREILKDILRVGLPSSLSQLSMSIAMFFLNSVAITAGGENGVAVFTSAWRITMLGIVPILGMAAATTSVTGAAYGERNVEKLETAYLYAIKIAFMIELAVVAFIMLFAPQVAYLFT-------IKGDLISALRTLPVFLVLTPFGMMTSAMFQGIGEGEKSLILTIFRTLVMQVGFAYIFVHYTTLGLRGVWIGIVIGNMVAAIVGFLWGRMRISALKKT 454
                                    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      |  -    |  363       373       383       393       403       413       423       433       443       453 
                                                                                                                                                                                                                                                                                                                                                                                    350     358                                                                                                


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3vvs B   0 xxVYSAVCLYV  10
                            ||       9 
                            0-ACE      
                             1-DPN
   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  (0, 0)

(no "SCOP Domain" information available for 3VVS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8U2X0_PYRFU | Q8U2X0)
molecular function
    GO:0015297    antiporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
    GO:0015238    drug transmembrane transporter activity    Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
biological process
    GO:0006855    drug transmembrane transport    The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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
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.

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q8U2X0_PYRFU | Q8U2X0: 3vvn 3vvo 3vvp 3vvr 3w4t 3wbn 4mlb

(-) Related Entries Specified in the PDB File

3vvn 3vvo 3vvp 3vvq 3vvr