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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PAPE (N-TERMINAL-DELETED) PILUS SUBUNIT BOUND TO A PEPTIDE CORRESPONDING TO THE N-TERMINAL EXTENSION OF THE PAPK PILUS SUBUNIT (RESIDUES 1-11) FROM UROPATHOGENIC E. COLI
 
Authors :  F. G. Sauer, J. S. Pinkner, G. Waksman, S. J. Hultgren
Date :  16 Oct 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin-Like Fold, Donor Strand Complementation, Donor Strand Exchange, Chaperone Priming, Pilus Fiber Assembly, Organelle Biogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. G. Sauer, J. S. Pinkner, G. Waksman, S. J. Hultgren
Chaperone Priming Of Pilus Subunits Facilitates A Topological Transition That Drives Fiber Formation
Cell(Cambridge, Mass. ) V. 111 543 2002
PubMed-ID: 12437927  |  Reference-DOI: 10.1016/S0092-8674(02)01050-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATURE FIMBRIAL PROTEIN PAPE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUE 25-173, RESIDUE 26-36 DELETED
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - PEPTIDE CORRESPONDING TO THE N-TERMINAL EXTENSION OF PROTEIN PAPK
    Chains: B, D
    Engineered: YES
    Fragment: RESIDUE 22-32
    Other Details: SYNTHESIZED PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1N12)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:15 -A:48
2C:15 -C:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N12)

(-) Exons   (0, 0)

(no "Exon" information available for 1N12)

(-) 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:138
 aligned with PAPE_ECOLX | P08407 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:138
                                    45        55        65        75        85        95       105       115       125       135       145       155       165        
           PAPE_ECOLX    36 IPACTVSNTTVDWQDVEIQTLSQNGNHEKEFTVNMRCPYNLGTMKVTITATNTYNNAILVQNTSNTSSDGLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYKGNMQNLIAGPFSATATLVASYS 173
               SCOP domains d1n12a_ A: PapE pilus subunit                                                                                                              SCOP domains
               CATH domains 1n12A00 A:1-149  [code=2.60.40.1090, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee..eeeeeeeee.hhh....eeeeeeeeeee.......eeeeee...ee..eee..........eeeeeeeeee..eeeee...........ee....eeeeeeeeeeeee.hhhhh..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n12 A   1 VPACTVSNTTVDWQDVEIQTLSQNGNHEKEFTVNmRCPYNLGTmKVTITATNTYNNAILVQNTSNTSSDGLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYKGNmQNLIAGPFSATATLVASYS 149
                            ||      21        31        41    |   51   |    61        71        81        91       101       111       121       131       141        
                            ||                               46-MSE   55-MSE                                                                    130-MSE               
                            1|                                                                                                                                        
                            13                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with PAPK_ECOL6 | P62533 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:11
                                    31 
           PAPK_ECOL6    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 B   1 SDVAFRGNLLD  11
                                    10 


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with PAPK_ECOLX | P62532 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:11
                                    31 
           PAPK_ECOLX    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 B   1 SDVAFRGNLLD  11
                                    10 


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with PRSK_ECOLX | P42191 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:11
                                    31 
           PRSK_ECOLX    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 B   1 SDVAFRGNLLD  11
                                    10 


Chain C from PDB  Type:PROTEIN  Length:136
 aligned with PAPE_ECOLX | P08407 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:138
                                    45        55        65        75        85        95       105       115       125       135       145       155       165        
           PAPE_ECOLX    36 IPACTVSNTTVDWQDVEIQTLSQNGNHEKEFTVNMRCPYNLGTMKVTITATNTYNNAILVQNTSNTSSDGLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYKGNMQNLIAGPFSATATLVASYS 173
               SCOP domains d1n12c_ C: PapE pilus subunit                                                                                                              SCOP domains
               CATH domains 1n12C00 C:1-149  [code=2.60.40.1090, no name defined]                                                                                      CATH domains
           Pfam domains (1) -Fimbrial-1n12C01 C:13-149                                                                                                                 Pfam domains (1)
           Pfam domains (2) -Fimbrial-1n12C02 C:13-149                                                                                                                 Pfam domains (2)
         Sec.struct. author ....ee..eeeeeeeee.hhh....eeeeeeeeeee.......eeeeee...ee..eee.......--.eeeeeeeeee..eeeee...........ee....eeeeeeeeeeeee.hhhhh..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n12 C   1 VPACTVSNTTVDWQDVEIQTLSQNGNHEKEFTVNmRCPYNLGTmKVTITATNTYNNAILVQNTSNT--DGLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYKGNmQNLIAGPFSATATLVASYS 149
                            ||      21        31        41    |   51   |    61        71     |  81        91       101       111       121       131       141        
                            1|                               46-MSE   55-MSE                77 80                                               130-MSE               
                            13                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with PAPK_ECOL6 | P62533 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:11
                                    31 
           PAPK_ECOL6    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
           Pfam domains (1) --Fimbrial- Pfam domains (1)
           Pfam domains (2) --Fimbrial- Pfam domains (2)
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 D   1 SDVAFRGNLLD  11
                                    10 


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with PAPK_ECOLX | P62532 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:11
                                    31 
           PAPK_ECOLX    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
           Pfam domains (1) --Fimbrial- Pfam domains (1)
           Pfam domains (2) --Fimbrial- Pfam domains (2)
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 D   1 SDVAFRGNLLD  11
                                    10 


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with PRSK_ECOLX | P42191 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:11
                                    31 
           PRSK_ECOLX    22 SDVAFRGNLLD  32
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
           Pfam domains (1) --Fimbrial- Pfam domains (1)
           Pfam domains (2) --Fimbrial- Pfam domains (2)
         Sec.struct. author .eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1n12 D   1 SDVAFRGNLLD  11
                                    10
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Adhesin (36)

(-) Gene Ontology  (3, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (PAPE_ECOLX | P08407)
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.
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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain B,D   (PRSK_ECOLX | P42191)
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.
cellular component
    GO:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain B,D   (PAPK_ECOL6 | P62533)
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.
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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain B,D   (PAPK_ECOLX | P62532)
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.
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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPE_ECOLX | P08407: 1n0l
        PAPK_ECOLX | P62532: 1pdk

(-) Related Entries Specified in the PDB File

1n0l THE CRYSTAL STRUCTURE OF THE PAPE (N-TERMINAL-DELETED) SUBUNIT BOUND TO THE PAPD CHAPERONE SHOWS THE STRUCTURE OF THE PAPE SUBUNIT BEFORE DONOR STRAND EXCHANGE.