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(-) Description

Title :  CRYSTAL STRUCTURE OF INTIMIN-TIR68 COMPLEX
 
Authors :  Y. Ma, F. Gao, D. -F. Li, G. F. Gao
Date :  12 Aug 08  (Deposition) - 18 Aug 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,M,N
Biol. Unit 1:  A,M,N  (1x)
Biol. Unit 2:  B,C,D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  M,N  (1x)
Biol. Unit 6:  C,D  (1x)
Keywords :  Protein-Protein Complex, Unique Intimin-Tir Trimer Intermediate, Cell Membrane, Cell Outer Membrane, Membrane, Transmembrane, Virulence, Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Ma, Q. Zou, G. F. Gao
Structural Insight Into The Interaction Between Intimin And Tir Of Enterohaemorrhagic E Coli: Evidence For A Dynamic Sequential Clustering-Aggregating-Reticulating Model
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTIMIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentD2-D3 DOMAIN, UNP RESIDUES 747-934
    GeneINTIMIN ADHERENCE PROTEIN 747-934
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83334
    SynonymATTACHING AND EFFACING PROTEIN, EAE PROTEIN, GAMMA-INTIMIN
 
Molecule 2 - PUTATIVE TRANSLOCATED INTIMIN RECEPTOR PROTEIN (TRANSLOCATED INTIMIN RECEPTOR TIR)
    ChainsM, N, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentIBD DOMAIN, UNP RESIDUES 269-336
    GeneTIR 269-336
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83334

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDMN
Biological Unit 1 (1x)A   MN
Biological Unit 2 (1x) BCD  
Biological Unit 3 (1x)A     
Biological Unit 4 (1x) B    
Biological Unit 5 (1x)    MN
Biological Unit 6 (1x)  CD  

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2ZQK)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:112 -A:186
2B:112 -B:186

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZQK)

(-) 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:183
 aligned with EAE_ECO57 | P43261 from UniProtKB/Swiss-Prot  Length:934

    Alignment length:183
                                   761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931   
            EAE_ECO57   752 FFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 934
               SCOP domains d2zqka1 A:6-94 automated matches                                                         d2zqka2 A:95-188 automated matches                                                             SCOP domains
               CATH domains 2zqkA01 A:6-95  [code=2.60.40.1080, no name defined]                                      2zqkA02 A:96-188 Mannose-Binding Protein A, subunit A                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eee.....ee.....ee...eee..ee.....eeeee.....eee....eeee.....eeeeeee....eeeeee.....eeeeeee.hhhhhhhhhh......hhhhhhhhhhhhhhhhh.........eeee..hhhhhhhheeeeee...eeeeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqk A   6 FFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 188
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with EAE_ECO57 | P43261 from UniProtKB/Swiss-Prot  Length:934

    Alignment length:184
                                   760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930    
            EAE_ECO57   751 TFFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 934
               SCOP domains d2zqkb1 B:5-94 automated matches                                                          d2zqkb2 B:95-188 automated matches                                                             SCOP domains
               CATH domains 2zqkB01 B:5-95  [code=2.60.40.1080, no name defined]                                       2zqkB02 B:96-188 Mannose-Binding Protein A, subunit A                                         CATH domains
           Pfam domains (1) -------Big_2-2zqkB03 B:12-90                                                          --Intimin_C-2zqkB01 B:93-188                                                                       Pfam domains (1)
           Pfam domains (2) -------Big_2-2zqkB04 B:12-90                                                          --Intimin_C-2zqkB02 B:93-188                                                                       Pfam domains (2)
         Sec.struct. author ......ee...eee.....ee...........ee..ee.....eeeee.....eee.....eee.....eeeeeee....eeeeee.......eeeee.hhhhhhhhh.......hhhhhhhhhhh.hhhhh.........eeee..hhhhhhh.eeeeee...eeeeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zqk B   5 TFFDELKIDNKVDIIGNNVRGELPNIWLQYGQFKLKASGGDGTYSWYSENTSIATVDASGKVTLNGKGSVVIKATSGDKQTVSYTIKAPSYMIKVDKQAYYADAMSICKNLLPSTQTVLSDIYDSWGAANKYSHYSSMNSITAWIKQTSSEQRSGVSSTYNLITQNPLPGVNVNTPNVYAVCVE 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:64
                                   282       292       302       312       322       332    
            TIR_ECO57   273 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2zqk C   5 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    14        24        34        44        54        64    

Chain D from PDB  Type:PROTEIN  Length:63
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:63
                                   283       293       303       313       323       333   
            TIR_ECO57   274 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2zqk D   6 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    15        25        35        45        55        65   

Chain M from PDB  Type:PROTEIN  Length:64
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:64
                                   282       292       302       312       322       332    
            TIR_ECO57   273 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 2zqk M   5 SATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    14        24        34        44        54        64    

Chain N from PDB  Type:PROTEIN  Length:63
 aligned with TIR_ECO57 | Q7DB77 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:63
                                   283       293       303       313       323       333   
            TIR_ECO57   274 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN 336
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2zqk N   6 ATETATRDQLTKEAFQNPDNQKVNIDELGNAIPSGVLKDDVVANIEEQAKAAGEEAKQQAIEN  68
                                    15        25        35        45        55        65   

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: C_Lectin (98)
(-)
Clan: E-set (290)

(-) Gene Ontology  (9, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EAE_ECO57 | P43261)
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.

Chain C,D,M,N   (TIR_ECO57 | Q7DB77)
molecular function
    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).
biological process
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        EAE_ECO57 | P432612zwk 3ncw 3ncx 4e1s 5g26
        TIR_ECO57 | Q7DB772zwk

(-) Related Entries Specified in the PDB File

2zwk INTIMIN-TIR90 COMPLEX