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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF ACRB IN COMPLEX WITH A NOVEL TRANSMEMBRANE HELIX.
 
Authors :  S. Tornroth-Horsefield, P. Gourdon, R. Horsefield, R. Neutze
Date :  22 Sep 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Drug Resistance, Multidrug Efflux, Transporter, Antiporter, Membrane Protein, Novel Transmembrane Helix, Acrb, Yajc, Inner Membrane, Membrane Protein/Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Tornroth-Horsefield, P. Gourdon, R. Horsefield, L. Brive, N. Yamamoto, H. Mori, A. Snijder, R. Neutze
Crystal Structure Of Acrb In Complex With A Single Transmembrane Subunit Reveals Another Twist.
Structure V. 15 1663 2007
PubMed-ID: 18073115  |  Reference-DOI: 10.1016/J.STR.2007.09.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACRIFLAVINE RESISTANCE PROTEIN B
    ChainsA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainJM109
 
Molecule 2 - UPF0092 MEMBRANE PROTEIN YAJC
    ChainsB
    FragmentUNP RESIDUES 19-55
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainJM109

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AIC2Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1AIC6Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:96 , GLY A:97 , ARG A:468BINDING SITE FOR RESIDUE AIC A 1109
2AC2SOFTWARELYS A:29 , ALA A:384 , ALA A:385 , PHE A:386 , GLY A:387BINDING SITE FOR RESIDUE AIC A 1110

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RDD)

(-) 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:1018
 aligned with ACRB_ECOLI | P31224 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:1036
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      
          ACRB_ECOLI      1 MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRK 1036
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rddA01 A:1-37,A:329-514             2rddA02 A:38-132,A:813-820 Multidrug efflux transporter AcrB pore domain                       2rddA03 A:133-179,A:276-328                    2rddA04 A:180-275 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains   2rddA03 A:133-179,A  :276-328                        2rddA01 A:1-37,A:329-514 Multidrug efflux transporter AcrB transmembrane domain                                                                                                           2rddA05 A:515-568,A:870-1036                          2rddA06 A:569-673 Multidrug efflux transporter AcrB pore domain                                                2rddA07 A:680-723,A:821-869                 2rddA08 A:724-812                                                                        2rddA02 2rddA07 A:680-723,A:821-869                      2rddA05 A:515-568,A:870-1036 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains                                                                CATH domains
               Pfam domains ACR_tran-2rddA01 A:1-1030                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ------ Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...........eeeeee.......hhhhhhhhhhhhh.......eeeee........eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee........hhhhhhhhhhhhhhhhhh.............eeeeeehhhhhhhh..hhhhhhhhhhhhh......ee............ee........hhhhhhh...ee.....eehhhhhheeeee......eeee..eeeee......--.hhhhhhhhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......-------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeee..........eeeeeeee.hhhhh.hhhhhhhhhhhhhhhhhh.....eeeeee......------.eeeeee....hhhhhhhhhhhhhhhhh.....---.........eee....hhhhhhhhh.hhhhhhhhhhhhhhheeeeeee....eeeeeeee.hhhh.hhhhhh..eee.....eee.hhh....eee......ee..eeeeeee..........hhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2rdd A    1 MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLA--ANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAK-------KGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVE------FDFELIDQAGLGHEKLTQARNQLLAEAAKHPDM---VRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRK 1036
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   |  |300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500 |     510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670  |    680       690       700       710 |   | 720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      
                                                                                                                                                                                                                                                                                                                               294  |                                                                                                                                                                                                          502     510                                                                                                                                                                673    680                             712 716                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                  297                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:37
 aligned with YAJC_ECOLI | P0ADZ7 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:37
                                    28        38        48       
          YAJC_ECOLI     19 SPMSLILMLVVFGLIFYFMILRPQQKRTKEHKKLMDS   55
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains YajC-2rddB01 B:19-55                  Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                2rdd B   19 SPMSLILMLVVFGLIFYFMILRPQQKRTKEHKKLMDS   55
                                    28        38        48       

   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 2RDD)

(-) CATH Domains  (6, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (14, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (ACRB_ECOLI | P31224)
molecular function
    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.
    GO:0015307    drug:proton antiporter activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + drug(in) = H+(in) + drug(out).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0046618    drug export    The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, out of a cell or organelle.
    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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    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.
    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.

Chain B   (YAJC_ECOLI | P0ADZ7)
cellular component
    GO:0031522    cell envelope Sec protein transport complex    A transmembrane protein complex involved in the translocation of proteins across the cytoplasmic membrane. In Gram-negative bacteria, Sec-translocated proteins are subsequently secreted via the type II, IV, or V secretion systems. Sec complex components include SecA, D, E, F, G, Y and YajC.
    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.
    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
        ACRB_ECOLI | P312241iwg 1oy6 1oy8 1oy9 1oyd 1oye 1t9t 1t9u 1t9v 1t9w 1t9x 1t9y 2dhh 2dr6 2drd 2gif 2hqc 2hqd 2hqf 2hqg 2hrt 2i6w 2j8s 2w1b 3aoa 3aob 3aoc 3aod 3d9b 3noc 3nog 3w9h 4c48 4cdi 4dx5 4dx6 4dx7 4k7q 4u8v 4u8y 4u95 4u96 4zit 4ziv 4ziw 4zjl 4zjo 4zjq 4zlj 4zll 4zln 5en5 5eno 5enp 5enq 5enr 5ens 5ent 5jmn 5nc5 5ng5 5o66 5v5s

(-) Related Entries Specified in the PDB File

1iwg ISOMORPHOUS (SYMMETRIC) STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.
1oy8 ISOMORPHOUS (SYMMETRIC) STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.
2dhh ASYMMETRIC STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.
2gif ASYMMETRIC STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.
2hqc ISOMORPHOUS (SYMMETRIC) STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.
2j8s ASYMMETRIC STRUCTURE OF ACRB WITHOUT THE NOVEL TM HELIX.