1N0L - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PAPD CHAPERONE (C-TERMINALLY 6X HISTIDINE-TAGGED) BOUND TO THE PAPE PILUS SUBUNIT (N-TERMINAL-DELETED) FROM UROPATHOGENIC E. COLI

Authors :   F. G. Sauer, J. S. Pinkner, G. Waksman, S. J. Hultgren

Date :   14 Oct 02 (Deposition) - 11 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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 Complemenation, Donor Strand Exchange, Chaperone Priming, Pilus Fiber Assembly (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)

Molecule 1 - CHAPERONE PROTEIN PAPD
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 22-239
	Gene	:	PAPD
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - MATURE FIMBRIAL PROTEIN PAPE
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 25-173, RESIDUES 26-36 DELETED
	Gene	:	PAPE
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1N0L)

Asymmetric Unit

No.	Residues
1	A:207	-	A:212
2	B:15	-	B:48
3	C:207	-	C:212
4	D:15	-	D:48

Asymmetric Unit

No.	Residues
1	Gly A:48	-	Pro A:49
2	Thr A:53	-	Pro A:54
3	Gly C:48	-	Pro C:49
4	Thr C:53	-	Pro C:54

(no "SAP(SNP)/Variant" information available for 1N0L)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PILI_CHAPERONE	PS00635	Gram-negative pili assembly chaperone signature.	PAPD_ECOLX	99-116	2	A:78-95 C:78-95

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PILI_CHAPERONE	PS00635	Gram-negative pili assembly chaperone signature.	PAPD_ECOLX	99-116	1	A:78-95 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PILI_CHAPERONE	PS00635	Gram-negative pili assembly chaperone signature.	PAPD_ECOLX	99-116	1	- C:78-95

(no "Exon" information available for 1N0L)

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
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Chain A from PDB  Type:PROTEIN  Length:215
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:215
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 236
               SCOP domains d1n0la1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d1n0la2 A:125-215 PapD                                                                      SCOP domains
               CATH domains 1n0lA01 A:1-121 PapD-like                                                                                                1n0lA02 A:122-212  [code=2.60.40.1070, no name defined]                                    --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee.....ee....eeee..eeee....eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhhheeeee..eeeeee.....eeeeeee.hhhhhhh.....eee...eeeeee.......eeee........eee.eee..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n0l A   1 AVSLDRTRAVFDGSEKSmTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSmVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVmLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 215
                                    10       |20        30        40        50        60     |  70        80        90       100       110       120       130       140       150       160       170 |     180       190       200       210     
                                            18-MSE                                          66-MSE                                                                                                   172-MSE

Chain B from PDB  Type:PROTEIN  Length:118
 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 d1n0lb_ B: PapE p      ilus subunit                                                                                                        SCOP domains
               CATH domains 1n0lB00 B:1-149        [code=2.60.40.1090, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee..eeee.....------......eeee.ee.........eeee...ee..eee..-----....eee..eeee..eeeee.....ee.......hhhhh.eeee...ee.---------..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n0l B   1 VPACTVSNTTVDWQDVE------NGNHEKEFTVNmRCPYNLGTmKVTITATNTYNNAILVQ-----SSDGLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYK---------PFSATATLVASYS 149
                            ||      21      |  -   |    41    |   51   |    61        71|     | 81        91       101       111       121     |   -     | 141        
                            1|             28     35         46-MSE   55-MSE           72    78                                              127       137            
                            13

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:215
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 236
               SCOP domains d1n0lc1 C:1-124 Pilus chaperone PapD, N-domain                                                                              d1n0lc2 C:125-215 PapD                                                                      SCOP domains
               CATH domains 1n0lC01 C:1-121 PapD-like                                                                                                1n0lC02 C:122-212  [code=2.60.40.1070, no name defined]                                    --- CATH domains
           Pfam domains (1) Pili_assembly_N-1n0lC01 C:1-121                                                                                          -------------------Pili_assembly_C-1n0lC03 C:141-204                               ----------- Pfam domains (1)
           Pfam domains (2) Pili_assembly_N-1n0lC02 C:1-121                                                                                          -------------------Pili_assembly_C-1n0lC04 C:141-204                               ----------- Pfam domains (2)
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee.....ee....eeee..eeee....eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eee.eee..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n0l C   1 AVSLDRTRAVFDGSEKSmTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSmVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVmLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 215
                                    10       |20        30        40        50        60     |  70        80        90       100       110       120       130       140       150       160       170 |     180       190       200       210     
                                            18-MSE                                          66-MSE                                                                                                   172-MSE

Chain D from PDB  Type:PROTEIN  Length:107
 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 d1n0ld_ D: Pa              pE pilus subunit                                                                                                SCOP domains
               CATH domains 1n0lD00 D:1-1              49  [code=2.60.40.1090, no name de        fined]                                                                CATH domains
           Pfam domains (1) -Fimbrial-1n0              lD01 D:13-149                                                                                                   Pfam domains (1)
           Pfam domains (2) -Fimbrial-1n0              lD02 D:13-149                                                                                                   Pfam domains (2)
         Sec.struct. author ....ee.......--------------..eeeeeee.........eeeee..ee..eeee.--------.eeeeeee....................eee....eeeeeeeeeee.---------..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n0l D   1 VPACTVSNTTVDW--------------EKEFTVNmRCPYNLGTmKVTITATNTYNNAILVQ--------GLLVYLYNSNAGNIGTAITLGTPFTPGKITGNNADKTISLHAKLGYK---------PFSATATLVASYS 149
                            ||      21  |      -       |41    |   51   |    61        71|       81        91       101       111       121     |   -     | 141        
                            1|         24             39     46-MSE   55-MSE           72       81                                           127       137            
                            13

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1070, no name defined] (29)

Escherichia coli. Organism_taxid: 562. (5)

1a	1n0lA02	A:122-212
1b	1n0lC02	C:122-212

Homologous Superfamily: [code=2.60.40.1090, no name defined] (10)

Escherichia coli. Organism_taxid: 562. (5)

2a	1n0lB00	B:1-149
2b	1n0lD00	D:1-149

Homologous Superfamily: PapD-like (38)

Escherichia coli. Organism_taxid: 562. (6)

3a	1n0lA01	A:1-121
3b	1n0lC01	C:1-121

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: Fimbrial (23)

Escherichia coli (15)

1a	Fimbrial-1n0lD01	D:13-149
1b	Fimbrial-1n0lD02	D:13-149

Clan: E-set (290)

Family: Pili_assembly_N (20)

Escherichia coli (8)

2a	Pili_assembly_N-1n0lC01	C:1-121
2b	Pili_assembly_N-1n0lC02	C:1-121

Clan: no clan defined [family: Pili_assembly_C] (20)

Family: Pili_assembly_C (20)

Escherichia coli (8)

3a	Pili_assembly_C-1n0lC03	C:141-204
3b	Pili_assembly_C-1n0lC04	C:141-204

Asymmetric Unit(hide GO term definitions)

Chain A,C (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 (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.

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	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ RasMol ]
		Gly C:48 - Pro C:49	[ RasMol ]
		Thr A:53 - Pro A:54	[ RasMol ]
		Thr C:53 - Pro C:54	[ RasMol ]

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1n12	THE 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 SHOWS THE STRUCTURE OF THE PAPE SUBUNIT AFTER DONOR STRAND EXCHANGE.

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