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(-) Description

Title :  CRYSTAL STRUCTURE OF IPGC IN COMPLEX WITH THE CHAPERONE BINDING REGION OF IPAB
 
Authors :  M. Lunelli, R. K. Lokareddy, A. Zychlinsky, M. Kolbe
Date :  06 Apr 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  P  (1x)
Biol. Unit 3:  Q  (1x)
Keywords :  Tetratricopeptide Repeat, Tpr, Chaperone, Chaperone Binding Region, Virulence, Membrane, Secreted, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lunelli, R. K. Lokareddy, A. Zychlinsky, M. Kolbe
Ipab-Ipgc Interaction Defines Binding Motif For Type Iii Secretion Translocator
Proc. Natl. Acad. Sci. Usa V. 106 9661 2009
PubMed-ID: 19478065  |  Reference-DOI: 10.1073/PNAS.0812900106

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN IPGC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-151
    Gene: IPGC
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: M90T
 
Molecule 2 - INVASIN IPAB
    Chains: P, Q
    Engineered: YES
    Fragment: CHAPERONE BINDING REGION OF IPAB, UNP RESIDUES 51-72
    Other Details: SYNTHESIZED PEPTIDE
    Synonym: 62 KDA ANTIGEN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABPQ
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   P 
Biological Unit 3 (1x):    Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:40 , ASN A:69 , ASP A:71 , LYS Q:71 , SER Q:72BINDING SITE FOR RESIDUE GOL A 152
2AC2SOFTWAREGLN A:81 , GLN A:112 , ARG A:116 , LEU Q:63BINDING SITE FOR RESIDUE GOL A 153
3AC3SOFTWARETYR B:40 , ASN B:69 , ASP B:71 , TYR B:72 , HOH B:160 , LYS P:68 , ALA P:69 , PRO P:70 , LYS P:71BINDING SITE FOR RESIDUE GOL B 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GZ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GZ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3GZ1)

(-) 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:144
 aligned with IPGC_SHIFL | P0A2U4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:144
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147    
           IPGC_SHIFL     8 NESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gz1 A   8 NESISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147    


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with IPGC_SHIFL | P0A2U4 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:142
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149  
           IPGC_SHIFL    10 SISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gz1 B  10 SISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHSNDEKLKIKAQSYLDAIQ 151
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149  


Chain P from PDB  Type:PROTEIN  Length:13
 aligned with IPAB_SHIFL | P18011 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:13
                                    69   
           IPAB_SHIFL    60 SNILIPELKAPKS  72
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 3gz1 P  60 SNILIPELKAPKS  72
                                    69   


Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with IPAB_SHIFL | P18011 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:10
                                    72
           IPAB_SHIFL    63 LIPELKAPKS  72
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 3gz1 Q  63 LIPELKAPKS  72
                                    72
   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 3GZ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GZ1)

(-) Gene Ontology  (10, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IPGC_SHIFL | P0A2U4)
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.
    GO:0006950    response to stress    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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain P,Q   (IPAB_SHIFL | P18011)
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:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. 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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  3gz1
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPAB_SHIFL | P18011: 3gz2 3u0c
        IPGC_SHIFL | P0A2U4: 3gyz 3gz2 3ks2

(-) Related Entries Specified in the PDB File

3gyz IPGC APO FORM
3gz2 IPGC IN COMPLEX WITH AN IPAB PEPTIDE