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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AIL, THE ATTACHMENT INVASION LOCUS PROTEIN OF YERSINIA PESTIS, IN COMPLEX WITH THE HEPARIN ANALOGUE SUCROSE OCTASULFATE
 
Authors :  S. Yamashita, P. Lukacik, N. Noinaj, S. K. Buchanan
Date :  17 Feb 11  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Barrel Protein, Attachment And Invasion Virulence, Laminin, Heparin, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, P. Lukacik, T. J. Barnard, N. Noinaj, S. Felek, T. M. Tsang, E. S. Krukonis, B. J. Hinnebusch, S. K. Buchanan
Structural Insights Into Ail-Mediated Adhesion In Yersinia Pestis.
Structure V. 19 1672 2011
PubMed-ID: 22078566  |  Reference-DOI: 10.1016/J.STR.2011.08.010

(-) Compounds

Molecule 1 - ATTACHMENT INVASION LOCUS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-182
    Gene: AIL, YPO2905
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: AIL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1C8E7Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SCR2Ligand/IonSUCROSE OCTASULFATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SCR1Ligand/IonSUCROSE OCTASULFATE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1C8E5Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SCR1Ligand/IonSUCROSE OCTASULFATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , TYR A:97 , HIS A:121 , LYS A:123 , LYS A:125 , SER A:137 , HOH A:190 , HOH A:198 , GLN B:38 , ARG B:40 , LYS B:47 , ASP B:49 , LYS B:50 , ASN B:51 , ARG B:78BINDING SITE FOR RESIDUE SCR A 1
2AC2SOFTWAREASN A:154 , TYR A:180 , TYR B:143BINDING SITE FOR RESIDUE C8E A 183
3AC3SOFTWAREGLU A:43 , PRO A:52 , LYS A:95 , ARG A:136 , LYS A:138 , HOH A:216BINDING SITE FOR RESIDUE C8E A 184
4AC4SOFTWAREILE A:32 , ALA A:178 , GLY A:179 , TYR A:180 , ALA B:101 , TYR B:114 , LEU B:117BINDING SITE FOR RESIDUE C8E B 1
5AC5SOFTWAREGLN A:38 , ARG A:40 , LYS A:47 , ASP A:49 , LYS A:50 , ASN A:51 , ARG A:78 , HOH A:230 , LYS B:95 , TYR B:97 , HIS B:121 , LYS B:123 , LYS B:125 , SER B:137 , HOH B:194 , HOH B:197BINDING SITE FOR RESIDUE SCR B 187
6AC6SOFTWAREVAL B:41 , PRO B:52 , THR B:76 , LYS B:95 , TYR B:96 , ARG B:136BINDING SITE FOR RESIDUE C8E B 183
7AC7SOFTWARETYR A:143 , ASN B:154 , TYR B:180BINDING SITE FOR RESIDUE C8E B 184
8AC8SOFTWAREALA A:101 , PRO A:103 , ALA B:178 , TYR B:180BINDING SITE FOR RESIDUE C8E B 185
9AC9SOFTWAREGLN B:38 , ARG B:40 , TYR B:161 , GLY B:172 , TRP B:174 , HOH B:199BINDING SITE FOR RESIDUE C8E B 186

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:49 -Lys A:50
2Asp B:49 -Lys B:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QRC)

(-) 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:153
 aligned with Q0WCZ9_YERPE | Q0WCZ9 from UniProtKB/TrEMBL  Length:182

    Alignment length:157
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       
         Q0WCZ9_YERPE    26 AEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
               SCOP domains d3qrca_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee..ee.....eeeeeeeeee....eeeeeeeeeeeeeeee..----.eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qrc A  26 MEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESV----LIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
                                    35        45        55        65        75        |-   |    95       105       115       125       135       145       155       165       175       
                                                                                     84   89                                                                                             


Chain A from PDB  Type:PROTEIN  Length:153
 aligned with Q8D0Z7_YERPE | Q8D0Z7 from UniProtKB/TrEMBL  Length:194

    Alignment length:157
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
         Q8D0Z7_YERPE    38 AEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 194
               SCOP domains d3qrca_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee..ee.....eeeeeeeeee....eeeeeeeeeeeeeeee..----.eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qrc A  26 MEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESV----LIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
                                    35        45        55        65        75        |-   |    95       105       115       125       135       145       155       165       175       
                                                                                     84   89                                                                                             


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q0WCZ9_YERPE | Q0WCZ9 from UniProtKB/TrEMBL  Length:182

    Alignment length:157
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       
         Q0WCZ9_YERPE    26 AEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
               SCOP domains d3qrcb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee..ee.....eeeeeeeeee....eeeeeeeeeeeeeeee...---.eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qrc B  26 MEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVD---LIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
                                    35        45        55        65        75        85   |    95       105       115       125       135       145       155       165       175       
                                                                                      85  89                                                                                             


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q8D0Z7_YERPE | Q8D0Z7 from UniProtKB/TrEMBL  Length:194

    Alignment length:157
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
         Q8D0Z7_YERPE    38 AEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVDGFKLIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 194
               SCOP domains d3qrcb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee..ee.....eeeeeeeeee....eeeeeeeeeeeeeeee...---.eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qrc B  26 MEGESSISIGYAQSRVKEDGYKLDKNPRGFNLKYRYEFNNDWGVIGSFAQTRRGFEESVD---LIDGDFKYYSVTAGPVFRINEYVSLYGLLGAGHGKAKFSSIFGQSESRSKTSLAYGAGLQFNPHPNFVIDASYEYSKLDDVKVGTWMLGAGYRF 182
                                    35        45        55        65        75        85   |    95       105       115       125       135       145       155       165       175       
                                                                                      85  89
   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, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q0WCZ9_YERPE | Q0WCZ9)
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.

Chain A,B   (Q8D0Z7_YERPE | Q8D0Z7)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q0WCZ9_YERPE | Q0WCZ9: 3qra
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        Q8D0Z7_YERPE | Q8D0Z7: 2n2l 2n2m 3qra

(-) Related Entries Specified in the PDB File

3qra APO AIL