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(-) Description

Title :  CRYSTAL STRUCTURE OF USHER PAPC TRANSLOCATION PORE
 
Authors :  Y. Huang, J. Deisenhofer
Date :  12 Dec 08  (Deposition) - 08 Sep 09  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Protein Translocase, Cell Membrane, Cell Outer Membrane, Fimbrium, Membrane, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Huang, B. S. Smith, L. X. Chen, R. H. Baxter, J. Deisenhofer
Insights Into Pilus Assembly And Secretion From The Structure And Functional Characterization Of Usher Papc.
Proc. Natl. Acad. Sci. Usa V. 106 7403 2009
PubMed-ID: 19380723  |  Reference-DOI: 10.1073/PNAS.0902789106

(-) Compounds

Molecule 1 - OUTER MEMBRANE USHER PROTEIN PAPC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD-PAPC
    Expression System Strain: SF120 STRAIN
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PAPC TRANSLOCATION CORE
    Gene: ESCHERICHIA COLI ENTEROBACTERIACEAE, PAPC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3FIP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIMBRIAL_USHERPS01151 Fimbrial biogenesis outer membrane usher protein signature.PAPC_ECOLX315-325
 		  2A:288-298
B:288-298
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIMBRIAL_USHERPS01151 Fimbrial biogenesis outer membrane usher protein signature.PAPC_ECOLX315-325
 		  1A:288-298
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIMBRIAL_USHERPS01151 Fimbrial biogenesis outer membrane usher protein signature.PAPC_ECOLX315-325
 		  1-
B:288-298

(-) Exons   (0, 0)

(no "Exon" information available for 3FIP)

(-) 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:436
 aligned with PAPC_ECOLX | P07110 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:491
                                   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662 
           PAPC_ECOLX   173 LMLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGPWRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLESDDRMLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGYGHETEGPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKSWRLSYSKRFDNADADITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNVADWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVFGLQGVAVGLSASRSKYLGRDNDSAYLRISVPLGTGTASYSGSMSNDRYVNMAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGGATIT 663
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee......eeeeeeeeeeee....eeeeeeee..eeee..---.eeee..eeeeeeeeeee....eeeeeeeee.........eeeeeeeee..----------.....eee....eeeeee..eeeeeee...eee...........eeeeeee........eeee............eeeeeeeee....-----..eeeeeeeeee....eeeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeee..--.eeeeeeeeeee...-------.eeeeeeee.....hhhhhhhhhh.......eeeeeeeeeeee.---..eeeeeeeeeee.....eeeeeeeeee..-------.eeeeeee..----....eeeeeeee..---.eeeeee..--.eeeeeeeeee..---.eeeeeeeeee-----.eeeeeeeeeee...eeeeeeeeee..-.eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------FIMBRIAL_US-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fip A 146 LMLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGPWRLRADYQGSQEQSRY---KTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLESDD----------APQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGY-----GPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIE--RTFQGKSWRLSYSKR-------ITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNV---NTSFNLQYSRQTYWDIRKTDYYTVSVNRYF-------VAVGLSASRS----RDNDSAYLRISVPL---TASYSGSMS--RYVNMAGYTDTFN---DSYSLNAGLNS-----SQRQINAYYSHRSPLANLSANIASLQK-YTSFGVSASGGATIT 636
                                   155       165       175       185       195|   |  205       215       225       235       245    |    -     | 265       275       285       295       305       315       325       335       345  |    355       365       375       385       395       405     | 415       425  |      -|      445       455       465       475   |   485       495       505      |  -    |  525   |   535       545 |   | 555   |  |565        |-  |    585  |    595       605       615    | |625       635 
                                                                            196 200                                               250        261                                                                                    348   354                                                      411  |           428     436                                        479 483                          512     520      529  534          547 551     559  |         574 578       588   594                       620 |              
                                                                                                                                                                                                                                                                                                      414                                                                                                                                                 562                                                         622              


Chain B from PDB  Type:PROTEIN  Length:384
 aligned with PAPC_ECOLX | P07110 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:490
                                   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662
           PAPC_ECOLX   173 LMLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGPWRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLESDDRMLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGYGHETEGPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKSWRLSYSKRFDNADADITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNVADWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVFGLQGVAVGLSASRSKYLGRDNDSAYLRISVPLGTGTASYSGSMSNDRYVNMAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGGATI 662
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.--..---.....ee..ee..ee.-.eeeeeeeeeeeee.----...eeeeeeeeeeeeeee.....eeeeeeeeee.......eeeeeeeeee.--......---...ee.......eeeeee..ee...........ee...--....eeeeeee.......eeeee.......-....eeeeeeeee..-------..eeeeeeeeee.--.eeee-.eeee..eeeeeeeeee....--.eeeeeeeeeee...-.eeeeeeee.--------------.eeeeee.....hhhhhhhh.........eeeeeee..------------.eeeeeee.....eeeeeeee-------------.eeeeee..----..eeeeee.----------.eee..--..eee..--------...eeee....----------.eeeee.....eeeeeeee...--....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------FIMBRIAL_US------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fip B 146 LMLDYNLNGT--RN---GDSHQFSYNGTVGGNL-PWRLRADYQGSQEQS----EKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLESD--MLPPRL---APQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDL--SVRGRLDVEVIEQNGRKKTFQVDTASVPYL-RPGQVRYKLVSGRSR-------GPVFATGEASWGL--QWSLY-GAVLAGDYNALAAGAGWDLGV--TLSADITQSVARIEG-RTFQGKSWRL--------------FAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTL------------LQYSRQTYWDIRKTDYYTVSV-------------VGLSASRSK----DNDSAYLRI----------YSGSMS--RYVNMAG--------LDSYSLNAGLN----------INAYYSHRSPLANLSANIASLQ--YTSFGVSASGGATI 635
                                   155  ||   165       175  | |  185        |-   |   205       215       225       235       245   |  |255 |   | 265       275       285       295  |  | 305       315       325    | |335       345|      355       365|  |   375       385       395  |    405      |415       | -         -  |    445       455       465       475         -  |    495       505  |      -      |525    |  535       | -       555   |  |565  |      - |     585 |       -  |    605       615   |  |625       635
                                   155  || 163            178 |           194  199                                               249  |  257 261                                  298  |                          330 |           346     354         366  | 373 |                 395  |           412 |      423            438                                  475          488                 508           522     530  535     543        554  559  |   568      577       587        598                  619  |             
                                      158|                  180                                                                     252                                              301                            332                                  369   375                    398             414                                                                                                                                                 562                                                         622             
                                       159
   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 3FIP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAPC_ECOLX | P07110)
molecular function
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPC_ECOLX | P07110: 2kt6 2vqi

(-) Related Entries Specified in the PDB File

2vqi THE SAME PROTEIN AS STRUCTURE OF THE P PILUS USHER (PAPC) TRANSLOCATION PORE BY REMAUT ET AL