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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P PILUS ROD SUBUNIT PAPA
 
Authors :  D. Verger, E. Bullitt, S. J. Hultgren, G. Waksman
Date :  02 Apr 07  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Donor Strand Complementation, Pili/N-Terminal Extension, Pilus Biogenesis, Donor-Strand Exchange, Nte, Dsc, Dse, Papa, Papd, Fimbria, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Verger, E. Bullitt, S. J. Hultgren, G. Waksman
Crystal Structure Of The P Pilus Rod Subunit Papa.
Plos Pathog. V. 3 E73 2007
PubMed-ID: 17511517  |  Reference-DOI: 10.1371/JOURNAL.PPAT.0030073

(-) Compounds

Molecule 1 - PERIPLASMID CHAPERONE PAPD PROTEIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 364106
    Other Details: WILD TYPE P PILUS CHAPERONE PAPD
    Strain: UTI89
 
Molecule 2 - PAP FIMBRIAL MAJOR PILIN PROTEIN
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: P PILUS ROD SUBUNIT PAPA
    Strain: J96
    Synonym: PAP PILI

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:142 , HOH A:2055 , ARG G:82 , TYR G:150 , SER G:174BINDING SITE FOR RESIDUE SO4 A1217
02AC2SOFTWAREGLU A:40 , ARG A:82 , TYR A:150 , SER A:174 , HOH A:2056 , VAL G:137 , ARG G:142BINDING SITE FOR RESIDUE SO4 A1218
03AC3SOFTWARELYS A:44 , ARG A:91 , THR E:47BINDING SITE FOR RESIDUE SO4 A1219
04AC4SOFTWAREGLN A:42 , GLU A:43 , LYS A:44BINDING SITE FOR RESIDUE SO4 A1220
05AC5SOFTWAREILE A:46 , THR A:47 , HOH A:2058 , LYS E:44 , SO4 E:1217BINDING SITE FOR RESIDUE SO4 A1221
06AC6SOFTWAREVAL C:137 , ARG C:142 , ARG E:82 , TYR E:150 , SER E:174BINDING SITE FOR RESIDUE SO4 C1217
07AC7SOFTWAREARG C:82 , TYR C:150 , SER C:174 , VAL E:137 , ARG E:142 , HOH E:2027BINDING SITE FOR RESIDUE SO4 C1218
08AC8SOFTWARELYS C:44 , ARG C:91 , THR G:47BINDING SITE FOR RESIDUE SO4 C1219
09AC9SOFTWARETHR A:47 , SO4 A:1221 , LYS E:44 , ARG E:91 , HOH E:2033BINDING SITE FOR RESIDUE SO4 E1217
10BC1SOFTWARELYS G:112 , MET G:172 , HOH G:2039 , GLN H:163BINDING SITE FOR RESIDUE SO4 G1217
11BC2SOFTWAREGLU G:43 , LYS G:44BINDING SITE FOR RESIDUE SO4 G1218
12BC3SOFTWARELYS G:44 , ARG G:91 , GLN G:108 , HOH G:2012BINDING SITE FOR RESIDUE SO4 G1219
13BC4SOFTWAREASN F:87 , ALA G:184 , ASN G:185BINDING SITE FOR RESIDUE SO4 G1220

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:207 -A:212
2B:22 -B:61
3C:207 -C:212
4D:22 -D:61
5E:207 -E:212
6F:22 -F:61
7G:207 -G:212
8H:22 -H:61

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Thr A:53 -Pro A:54
3Gly C:48 -Pro C:49
4Thr C:53 -Pro C:54
5Gly E:48 -Pro E:49
6Thr E:53 -Pro E:54
7Gly G:48 -Pro G:49
8Thr G:53 -Pro G:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UY7)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116
 
 
 		  4A:78-95
C:78-95
E:78-95
G:78-95
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116
 
 
 		  1A:78-95
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116
 
 
 		  1-
C:78-95
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116
 
 
 		  1-
-
E:78-95
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116
 
 
 		  1-
-
-
G:78-95

(-) Exons   (0, 0)

(no "Exon" information available for 2UY7)

(-) 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:217
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7a2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7A01 A:1-121 PapD-like                                                                                                2uy7A02 A:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain A from PDB  Type:PROTEIN  Length:217
 aligned with Q1R2W9_ECOUT | Q1R2W9 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7a2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7A01 A:1-121 PapD-like                                                                                                2uy7A02 A:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:156
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
           PAPA_ECOLX    30 QGKVTFNGTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy7b1 B:8-163 Pap fimbrial major pilin protein PapA                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eee.............hhhhhhh......eeeeeeee.................eeeeee..ee..eeeeee......eeeeee.......................eeeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uy7 B   8 QGKVTFNNTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7c1 C:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7c2 C:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7C01 C:1-121 PapD-like                                                                                                2uy7C02 C:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 C   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with Q1R2W9_ECOUT | Q1R2W9 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7c1 C:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7c2 C:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7C01 C:1-121 PapD-like                                                                                                2uy7C02 C:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 C   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain D from PDB  Type:PROTEIN  Length:154
 aligned with PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:156
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
           PAPA_ECOLX    30 QGKVTFNGTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy7d_ D: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eee.............hhhhhhh......eeeeeeee..hhhhh..--......eeeeee..................eeeeee.......................eeeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uy7 D   8 QGKVTFNNTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKG--GAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    17        27        37        47        57        67|  |    77        87        97       107       117       127       137       147       157      
                                                                                       68 71                                                                                            


Chain E from PDB  Type:PROTEIN  Length:217
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7e1 E:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7e2 E:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7E01 E:1-121 PapD-like                                                                                                2uy7E02 E:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 E   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain E from PDB  Type:PROTEIN  Length:217
 aligned with Q1R2W9_ECOUT | Q1R2W9 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7e1 E:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7e2 E:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7E01 E:1-121 PapD-like                                                                                                2uy7E02 E:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 E   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain F from PDB  Type:PROTEIN  Length:156
 aligned with PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:156
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
           PAPA_ECOLX    30 QGKVTFNGTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy7f_ F: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eee.............hhhhhhh......eeeeeeee..hhhhh..........eeeeee..ee..eeeeee......eeeeeee..ee..................eeeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uy7 F   8 QGKVTFNNTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      


Chain G from PDB  Type:PROTEIN  Length:217
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7g1 G:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7g2 G:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7G01 G:1-121 PapD-like                                                                                                2uy7G02 G:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
           Pfam domains (1) Pili_assembly_N-2uy7G01 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G05 G:141-204                               ------------- Pfam domains (1)
           Pfam domains (2) Pili_assembly_N-2uy7G02 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G06 G:141-204                               ------------- Pfam domains (2)
           Pfam domains (3) Pili_assembly_N-2uy7G03 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G07 G:141-204                               ------------- Pfam domains (3)
           Pfam domains (4) Pili_assembly_N-2uy7G04 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G08 G:141-204                               ------------- Pfam domains (4)
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeeee....ee....eeee..eeee....eeeeeeee.hhhhhh.......................eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 G   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain G from PDB  Type:PROTEIN  Length:217
 aligned with Q1R2W9_ECOUT | Q1R2W9 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy7g1 G:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy7g2 G:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy7G01 G:1-121 PapD-like                                                                                                2uy7G02 G:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
           Pfam domains (1) Pili_assembly_N-2uy7G01 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G05 G:141-204                               ------------- Pfam domains (1)
           Pfam domains (2) Pili_assembly_N-2uy7G02 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G06 G:141-204                               ------------- Pfam domains (2)
           Pfam domains (3) Pili_assembly_N-2uy7G03 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G07 G:141-204                               ------------- Pfam domains (3)
           Pfam domains (4) Pili_assembly_N-2uy7G04 G:1-121                                                                                          -------------------Pili_assembly_C-2uy7G08 G:141-204                               ------------- Pfam domains (4)
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeeee....ee....eeee..eeee....eeeeeeee.hhhhhh.......................eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy7 G   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain H from PDB  Type:PROTEIN  Length:154
 aligned with PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:156
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
           PAPA_ECOLX    30 QGKVTFNGTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy7h_ H: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---Fimbrial-2uy7H01 H:11-163                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ---Fimbrial-2uy7H02 H:11-163                                                                                                                                 Pfam domains (2)
           Pfam domains (3) ---Fimbrial-2uy7H03 H:11-163                                                                                                                                 Pfam domains (3)
           Pfam domains (4) ---Fimbrial-2uy7H04 H:11-163                                                                                                                                 Pfam domains (4)
         Sec.struct. author ...............eee......eee....hhhhhh.......eeeeeeee...hhhhhh--......eeeeee..ee..eeeeee......eeeeeee..ee..................eeeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uy7 H   8 QGKVTFNNTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKG--GAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    17        27        37        47        57        67|  |    77        87        97       107       117       127       137       147       157      
                                                                                       68 71
   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  (4, 12)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (3, 12)

Asymmetric Unit
(-)
Clan: Adhesin (36)
(-)
Clan: E-set (290)
(-)
Clan: no clan defined [family: Pili_assembly_C] (20)

(-) Gene Ontology  (8, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (Q1R2W9_ECOUT | Q1R2W9)
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0043711    pilus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A,C,E,G   (PAPD_ECOLX | P15319)
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0043711    pilus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B,D,F,H   (PAPA_ECOLX | P04127)
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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  2uy7
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  PAPD_ECOLX | P15319
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPA_ECOLX | P04127: 2uy6 5flu
        PAPD_ECOLX | P15319: 1n0l 1pdk 1qpp 1qpx 2j2z 2j7l 2uy6 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93
UniProtKB/TrEMBL
        Q1R2W9_ECOUT | Q1R2W9: 2uy6 2w07 2wmp

(-) Related Entries Specified in the PDB File

1n0l CRYSTAL STRUCTURE OF THE PAPD CHAPERONE (C- TERMINALLY 6XHISTIDINE-TAGGED) BOUND TO THE PAPE PILUS SUBUNIT (N-TERMINAL-DELETED) FROM UROPATHOGENIC E. COLI
1pdk PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS
1qpp CRYSTAL STRUCTURES OF SELF CAPPING PAPD CHAPERONE HOMODIMERS
1qpx CRYSTAL STRUCTURES OF SELF-CAPPING PAPD CHAPERONE HOMODIMERS
2j2z X-RAY STRUCTURE OF THE CHAPERONE PAPD IN COMPLEX WITH THE PILUS TERMINATOR SUBUNIT PAPH AT 2.3 ANGSTROM RESOLUTION
2j7l E. COLI P PILUS CHAPERONE PAPD IN COMPLEX WITH A PILUS BIOGENESIS INHIBITOR, PILICIDE 2C
2uy6 CRYSTAL STRUCTURE OF THE P PILUS ROD SUBUNIT PAPA
3dpa PAPD