Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF INTIMIN IN COMPLEX WITH TRANSLOCATED INTIMIN RECEPTOR (TIR) INTIMIN-BINDING DOMAIN
 
Authors :  Y. Luo, E. A. Frey, R. A. Pfuetzner, A. L. Creagh, D. G. Knoechel, C. A. Haynes, B. B. Finlay, N. C. J. Strynadka
Date :  14 May 00  (Deposition) - 12 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  I,T
Biol. Unit 1:  I (1x),T (2x)
Keywords :  Immunoglobulin-Like Fold, C-Type Lectin-Like Fold, Four- Helix Bundle, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Luo, E. A. Frey, R. A. Pfuetzner, A. L. Creagh, D. G. Knoechel, C. A. Haynes, B. B. Finlay, N. C. Strynadka
Crystal Structure Of Enteropathogenic Escherichia Coli Intimin-Receptor Complex.
Nature V. 405 1073 2000
PubMed-ID: 10890451  |  Reference-DOI: 10.1038/35016618
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTIMIN
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (282 RESIDUES)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - TRANSLOCATED INTIMIN RECEPTOR
    Chains: T
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: INTIMIN-BINDING DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TIR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : IT
Biological Unit 1 (2x): I (1x)T (2x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F02)

(-) Sites  (0, 0)

(no "Site" information available for 1F02)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1I:860 -I:937

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F02)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F02)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIG1PS51127 Big-1 (bacterial Ig-like domain 1) domain profile.EAE_ECO27560-653
660-751		  1-
I:660-751
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIG1PS51127 Big-1 (bacterial Ig-like domain 1) domain profile.EAE_ECO27560-653
660-751		  2-
I:660-751

(-) Exons   (0, 0)

(no "Exon" information available for 1F02)

(-) 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 I from PDB  Type:PROTEIN  Length:282
 aligned with EAE_ECO27 | P19809 from UniProtKB/Swiss-Prot  Length:939

    Alignment length:282
                                   667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937  
            EAE_ECO27   658 ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK 939
               SCOP domains d1f02i1 I:658-752 Intimin                                                                      d1f02i2 I:753-841 Intimin                                                                d1f02i3 I:842-939 Intimin                                                                          SCOP domains
               CATH domains 1f02I01 I:658-752  [code=2.60.40.920, no name defined]                                         1f02I02 I:753-841  [code=2.60.40.1080, no name defined]                                  1f02I03 I:842-939 Mannose-Binding Protein A, subunit A                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...eee......eeeeeeeee..ee....eeeee....ee...eee.....eeeeeee....eee..eeee......ee...eeee...eeeeeeeee.....ee....eee...eeeeeee.....eeeee.....eee.....eeee.....eeeeeee....eeeeee....eeeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhheeeeee...eeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --BIG1  PDB: I:660-751 UniProt: 660-751                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f02 I 658 ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK 939
                                   667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937  


Chain T from PDB  Type:PROTEIN  Length:66
 aligned with Q9KWH9_ECOLX | Q9KWH9 from UniProtKB/TrEMBL  Length:552

    Alignment length:66
                                   280       290       300       310       320       330      
         Q9KWH9_ECOLX   271 PDQAANAAESATKDQLTQEAFKNPENQKVNIDANGNAIPSGELKDDIVEQIAQQAKEAGEVARQQA 336
               SCOP domains d1f02t_ T:                                                         SCOP domains
               CATH domains 1f02T00 T:271-336 Translocated Intimin Receptor; Chain T           CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeeeeeeehhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1f02 T 271 MDQAANAAESATKDQLTQEAFKNPENQKVNIDANGNAIPSGELKDDIVEQIAQQAKEAGEVARQQA 336
                                   280       290       300       310       320       330
   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  (3, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Peptides (792)

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F02)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain I   (EAE_ECO27 | P19809)
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 T   (Q9KWH9_ECOLX | Q9KWH9)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1f02)
 
  Sites
(no "Sites" information available for 1f02)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f02)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1f02
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EAE_ECO27 | P19809
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9KWH9_ECOLX | Q9KWH9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EAE_ECO27 | P19809
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9KWH9_ECOLX | Q9KWH9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EAE_ECO27 | P19809: 1e5u 1f00 2mpw

(-) Related Entries Specified in the PDB File

1cwv CRYSTAL STRUCTURE OF INVASIN FRAGMENT.
1f00 CRYSTAL STRUCTURE OF THE SAME FRAGMENT OF INTIMIN.
1inm NMR STRUCTURE FO SIMILAR FRAGMENT OF INTIMIN.