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(-) Description

Title :  ELECTRON MICROSCOPY MODEL OF THE SAF PILUS- TYPE B
 
Authors :  O. Salih, H. Remaut, G. Waksman, E. V. Orlova
Date :  07 Apr 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  17.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Safa Protein Polymer, Type B Saf Pilus, Fibril Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Salih, H. Remaut, G. Waksman, E. V. Orlova
Structural Analysis Of The Saf Pilus By Electron Microscopy And Image Processing.
J. Mol. Biol. V. 379 174 2008
PubMed-ID: 18448124  |  Reference-DOI: 10.1016/J.JMB.2008.03.056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Vector Type: PLASMID
    Fragment: CORE PILIN DOMAIN, N-TERMINAL DELETED, UNP RESIDUES 48-170
    Gene: SAFA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Strain: LT2
    Synonym: SAFA PILUS SUBUNIT
 
Molecule 2 - OUTER MEMBRANE PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Vector Type: PLASMID
    Fragment: CORE PILIN DOMAIN, UNP RESIDUES 27-170
    Gene: SAFA
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Strain: LT2
    Synonym: SAFA PILUS SUBUNIT
 
Molecule 3 - OUTER MEMBRANE PROTEIN
    Chains: C
    Engineered: YES
    Fragment: N-TERMINAL EXTENSION, UNP RESIDUES 27-45
    Other Details: SAFANTE-N-TERMINAL EXTENSION
    Synonym: SAFA N-TERMINAL EXTENSION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CRF)

(-) Sites  (0, 0)

(no "Site" information available for 3CRF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:18 -Ser B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CRF)

(-) Sequences/Alignments

Asymmetric/Biological 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:123
 aligned with Q8ZRK4_SALTY | Q8ZRK4 from UniProtKB/TrEMBL  Length:170

    Alignment length:123
                                    57        67        77        87        97       107       117       127       137       147       157       167   
         Q8ZRK4_SALTY    48 DLTVSLIPVSGLKAGKNAPSAKIAKLVVNSTTLKEFGVRGISNNVVDSTGTAWRVAGKNTGKEIGVGLSSDSLRRSDSTEKWNGVNWMTFNSNDTLDIVLTGPAQNVTADTYPITLDVVGYQP 170
               SCOP domains d3crfa1 A:22-142 SafA pilus subunit                                                                                      -- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......ee.....eeeeeeee.....eeeeeee..........eeeee......eeeeeehhhhhhh..eeeee..eeeeeee..eeeeeee.....ee...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3crf A  22 DLTVSLIPVSGLKAGKNAPSAKIAKLVVNSTTLKEFGVRGISNNVVDSTGTAWRVAGKNTGKEIGVGLSSDSLRRSDSTEKWNGVNWMTFNSNDTLDIVLTGPAQNVTADTYPITLDVVGYQP 144
                                    31        41        51        61        71        81        91       101       111       121       131       141   


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Q8ZRK4_SALTY | Q8ZRK4 from UniProtKB/TrEMBL  Length:170

    Alignment length:144
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166    
         Q8ZRK4_SALTY    27 GSFLPNSEQQKSVDIVFSSPQDLTVSLIPVSGLKAGKNAPSAKIAKLVVNSTTLKEFGVRGISNNVVDSTGTAWRVAGKNTGKEIGVGLSSDSLRRSDSTEKWNGVNWMTFNSNDTLDIVLTGPAQNVTADTYPITLDVVGYQP 170
               SCOP domains ---------d3crfb1 B:10-142 SafA pilus subunit                                                                                                  -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee.......eeeeee......ee.....eeeeeeee.....eeeeeee..ee......eeeee......eeeeeehhhhhhh..eeeee..eeeeeee...eeeeee.....ee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3crf B   1 GSFLPNSEQQKSVDIVFSSPQDLTVSLIPVSGLKAGKNAPSAKIAKLVVNSTTLKEFGVRGISNNVVDSTGTAWRVAGKNTGKEIGVGLSSDSLRRSDSTEKWNGVNWMTFNSNDTLDIVLTGPAQNVTADTYPITLDVVGYQP 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain C from PDB  Type:PROTEIN  Length:19
 aligned with Q8ZRK4_SALTY | Q8ZRK4 from UniProtKB/TrEMBL  Length:170

    Alignment length:19
                                    36         
         Q8ZRK4_SALTY    27 GSFLPNSEQQKSVDIVFSS  45
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 3crf C   1 GSFLPNSEQQKSVDIVFSS  19
                                    10
   Legend:   → Mismatch (orange background)
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    → 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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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  Cis Peptide Bonds
    Ser B:18 - Ser B:19   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q8ZRK4_SALTY | Q8ZRK4: 2cny 2cnz 2co1 2co2 2co3 2co4 2co6 2co7 3cre

(-) Related Entries Specified in the PDB File

2co4 SALMONELLA ENTERICA SAFA PILIN IN COMPLEX WITH A 19-RESIDUE SAFA NTE PEPTIDE
3cre ELECTRON MICROSCOPY MODEL OF THE SAF PILUS - TYPE A