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(-) Description

Title :  TETRAMER OF IPAD, MODIFIED FROM 2J0O, FITTED INTO NEGATIVE STAIN ELECTRON MICROSCOPY RECONSTRUCTION OF THE WILD TYPE TIP COMPLEX FROM THE TYPE III SECRETION SYSTEM OF SHIGELLA FLEXNERI
 
Authors :  M. Cheung, D. -K. Shen, F. Makino, T. Kato, D. Roehrich, I. Martinez-Arg M. L. Walker, I. Murillo, X. Liu, M. Pain, J. Brown, G. Frazer, J. Mantel T. Todd, R. B. Sessions, K. Namba, A. J. Blocker
Date :  21 Oct 14  (Deposition) - 10 Dec 14  (Release) - 14 Jan 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  2.12
Chains :  Asym. Unit :  D  (4x)
Biol. Unit 1:  D  (1x)
Keywords :  Cell Invasion, Tip Complex, Type Iii Secretion System, Shigella Flexneri, Wild Type, Ipad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Cheung, D. Shen, F. Makino, T. Kato, A. D. Roehrich, I. Martinez-Argudo, M. L. Walker, I. Murillo, X. Liu, M. Pain, J. Brown G. Frazer, J. Mantell, P. Mina, T. Todd, R. B. Sessions, K. Namba, A. J. Blocker
Three-Dimensional Electron Microscopy Reconstruction And Cysteine-Mediated Crosslinking Provide A Model Of The T3Ss Needle Tip Complex.
Mol. Microbiol. V. 95 31 2015
PubMed-ID: 25353930  |  Reference-DOI: 10.1111/MMI.12843
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INVASIN IPAD
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: COILDED-COIL AND GLOBULAR DOMAIN, UNP RESIDUES 125-332
    Organism Scientific: SHIGELLA FLEXNERI 5A STR. M90T
    Organism Taxid: 1086030
    Other Details: YES [LACKING FIRST 124 AA AND WITH LAST 10 AA MODELLED INTO HELIX]
    Synonym: 36 KDA MEMBRANE ANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (4x): D
Biological Unit 1 (1x): D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4D3E)

(-) Sites  (0, 0)

(no "Site" information available for 4D3E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D3E)

(-) Cis Peptide Bonds  (5, 20)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4Gly D:182 -Asn D:183
21, 2, 3, 4Asn D:183 -Asp D:184
31, 2, 3, 4Gly D:185 -Asn D:186
41, 2, 3, 4Tyr D:212 -Pro D:213
51, 2, 3, 4Asn D:266 -Gly D:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_IPAD_SHIFL_003 *A136DIPAD_SHIFL  ---  ---DA136D
2UniProtVAR_IPAD_SHIFL_004 *N140KIPAD_SHIFL  ---  ---DN140K
3UniProtVAR_IPAD_SHIFL_005 *D144NIPAD_SHIFL  ---  ---DD144N
4UniProtVAR_IPAD_SHIFL_006 *N193KIPAD_SHIFL  ---  ---DN193K
5UniProtVAR_IPAD_SHIFL_007 *Q220KIPAD_SHIFL  ---  ---DQ220K
6UniProtVAR_IPAD_SHIFL_008 *Q239EIPAD_SHIFL  ---  ---DQ239E
7UniProtVAR_IPAD_SHIFL_009 *S247NIPAD_SHIFL  ---  ---DS247N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_IPAD_SHIFL_003 *A136DIPAD_SHIFL  ---  ---DA136D
2UniProtVAR_IPAD_SHIFL_004 *N140KIPAD_SHIFL  ---  ---DN140K
3UniProtVAR_IPAD_SHIFL_005 *D144NIPAD_SHIFL  ---  ---DD144N
4UniProtVAR_IPAD_SHIFL_006 *N193KIPAD_SHIFL  ---  ---DN193K
5UniProtVAR_IPAD_SHIFL_007 *Q220KIPAD_SHIFL  ---  ---DQ220K
6UniProtVAR_IPAD_SHIFL_008 *Q239EIPAD_SHIFL  ---  ---DQ239E
7UniProtVAR_IPAD_SHIFL_009 *S247NIPAD_SHIFL  ---  ---DS247N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D3E)

(-) Exons   (0, 0)

(no "Exon" information available for 4D3E)

(-) 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 D from PDB  Type:PROTEIN  Length:208
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:208
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        
           IPAD_SHIFL   125 GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSCTDTDKLFLHF 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......eeehhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeeee....eeeee.hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------D---K---N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3e D 125 GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSCTDTDKLFLHF 332
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324
   Legend:   → Mismatch (orange background)
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  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 4D3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D3E)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain D   (IPAD_SHIFL | P18013)
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.

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  Cis Peptide Bonds
    Asn D:183 - Asp D:184   [ RasMol ]  
    Asn D:266 - Gly D:267   [ RasMol ]  
    Gly D:182 - Asn D:183   [ RasMol ]  
    Gly D:185 - Asn D:186   [ RasMol ]  
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  4d3e
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 Related Entries

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

UniProtKB/Swiss-Prot
        IPAD_SHIFL | P18013: 2j0n 2j0o 2jaa 3r9v

(-) Related Entries Specified in the PDB File

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