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(-) Description

Title :  SOLID-STATE NMR STRUCTURE OF THE MEMBRANE ANCHOR DOMAIN OF THE TRIMERIC AUTOTRANSPORTER YADA
 
Authors :  S. A. Shahid, B. Bardiaux, W. T. Franks, M. Habeck, D. Linke, B. Van Ross
Date :  30 Nov 11  (Deposition) - 07 Nov 12  (Release) - 26 Dec 12  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A,B,C  (20x)
Biol. Unit 1:  A,B,C  (1x)
Keywords :  Trimeric Autotransporter, Membrane Protein, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Shahid, B. Bardiaux, W. T. Franks, L. Krabben, M. Habeck, B. J. Van Rossum, D. Linke
Membrane-Protein Structure Determination By Solid-State Nmr Spectroscopy Of Microcrystals.
Nat. Methods V. 9 1212 2012
PubMed-ID: 23142870  |  Reference-DOI: 10.1038/NMETH.2248

(-) Compounds

Molecule 1 - ADHESIN YADA
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 OMP8
    Expression System Taxid: 511693
    Expression System Vector: PUC-A-1
    Fragment: OUTER MEMBRANE REGION, RESIDUES 333-422
    Gene: YADA, YEP0066
    Organism Scientific: YERSINIA ENTEROCOLITICA SUBSP. ENTEROCOLITICA
    Organism Taxid: 393305
    Strain: 8081

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit (20x): ABC
Biological Unit 1 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LME)

(-) Sites  (0, 0)

(no "Site" information available for 2LME)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LME)

(-) 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:105
 aligned with YADA_YERE8 | A1JUB7 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:126
                                   306       316       326       336       346       356       366       376       386       396       406       416      
           YADA_YERE8   297 ADSKSSHTLQTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 422
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-------..........hh--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeeeeee......eeeeeee...eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2lme A   1 GD-------QASWSHPQFEKG--------------AHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 105
                             |       3        13|        -     |  19        29        39        49        59        69        79        89        99      
                             2       3         14             15                                                                                          


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with YADA_YERE8 | A1JUB7 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:126
                                   306       316       326       336       346       356       366       376       386       396       406       416      
           YADA_YERE8   297 ADSKSSHTLQTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 422
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-------..........hh--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeeeeee......eeeeeee...eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2lme B   1 GD-------QASWSHPQFEKG--------------AHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 105
                             |       3        13|        -     |  19        29        39        49        59        69        79        89        99      
                             2       3         14             15                                                                                          


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with YADA_YERE8 | A1JUB7 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:126
                                   306       316       326       336       346       356       366       376       386       396       406       416      
           YADA_YERE8   297 ADSKSSHTLQTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 422
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-------..........hh--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee..eeeeeeeeeeee......eeeeeee...eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2lme C   1 GD-------QASWSHPQFEKG--------------AHKFRQLDNRLDKLDTRVDKGLASSAALNSLFQPYGVGKVNFTAGVGGYRSSQALAIGSGYRVNESVALKAGVAYAGSSDVMYNASFNIEW 105
                             |       3        13|        -     |  19        29        39        49        59        69        79        89        99      
                             2       3         14             15
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  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 2LME)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LME)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (YADA_YERE8 | A1JUB7)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    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:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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