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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF SELF CAPPING PAPD CHAPERONE HOMODIMERS

Authors :   D. L. Hung, J. S. Pinkner, S. D. Knight, S. J. Hultgren

Date :   28 May 99 (Deposition) - 07 Jul 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Barrel, Immunoglobulin Fold Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. L. Hung, J. S. Pinkner, S. D. Knight, S. J. Hultgren
Structural Basis Of Chaperone Self-Capping In P Pilus Biogenesis.
Proc. Natl. Acad. Sci. Usa V. 96 8178 1999
PubMed-ID: 10393968 | Reference-DOI: 10.1073/PNAS.96.14.8178
(for further references see the PDB file header)

Molecule 1 - PAPD CHAPERONE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QPP)

(no "Site" information available for 1QPP)

Asymmetric/Biological Unit

No.	Residues
1	A:207	-	A:212
2	B:207	-	B:212

Asymmetric/Biological Unit

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

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

Asymmetric/Biological 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 B:78-95

(no "Exon" information available for 1QPP)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:207
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:214
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSV 235
               SCOP domains d1qppa1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d1qppa2 A:125-214 PapD                                                                     SCOP domains
               CATH domains 1qppA01 A:1-121 PapD-like                                                                                                1qppA02 A:122-214  [code=2.60.40.1070, no name defined]                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee............eeeeeeee.........................eeee..........eeeeeeee.hhhhhh..................-------.............hhhhh.....hhhhh.eeeee..eeeeee.....eeeeeee..hhhhhh.....eee...eeeeee.......eeeee.......eee.eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qpp A   1 AVSLDRTAAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLDPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPR-------QIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSV 214
                                    10        20        30        40        50        60        70        80        90     |   -   |   110       120       130       140       150       160       170       180       190       200       210    
                                                                                                                          96     104

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:214
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSV 235
               SCOP domains d1qppb1 B:1-122 Pilus chaperone PapD, N-domain                                                                            --d1qppb2 B:125-214 PapD                                                                     SCOP domains
               CATH domains 1qppB01 B:1-121 PapD-like                                                                                                1  qppB02 B:122-213  [code=2.60.40.1070, no name defined]                                   - CATH domains
           Pfam domains (1) Pili_assembly_N-1qppB01 B:1-121                                                                                          -------------------Pili_assembly_C-1qppB03 B:141-204                               ---------- Pfam domains (1)
           Pfam domains (2) Pili_assembly_N-1qppB02 B:1-121                                                                                          -------------------Pili_assembly_C-1qppB04 B:141-204                               ---------- Pfam domains (2)
         Sec.struct. author .eee............eeeeeeee.........................eeee..........eeeeeeee.hhhhhh......................................hhhhh.--..hhhhhheeeee..eeeee......eeeeeee.............eee....eeeee.......eeeee.......eee.eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qpp B   1 AVSLDRTAAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLDPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKT--NEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSV 214
                                    10        20        30        40        50        60        70        80        90       100       110       120 |  |  130       140       150       160       170       180       190       200       210    
                                                                                                                                                   122  |                                                                                         
                                                                                                                                                      125

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: Periplasmic chaperone C-domain (38)

Family: Periplasmic chaperone C-domain (33)

Protein domain: PapD (14)

Escherichia coli [TaxId: 562] (14)

1a	d1qppa2	A:125-214
1b	d1qppb2	B:125-214

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: PapD-like (47)

Family: Pilus chaperone (36)

Protein domain: Pilus chaperone PapD, N-domain (14)

Escherichia coli [TaxId: 562] (14)

2a	d1qppa1	A:1-124
2b	d1qppb1	B:1-122

Asymmetric/Biological 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. (4)

1a	1qppB02	B:122-213
1b	1qppA02	A:122-214

Homologous Superfamily: PapD-like (38)

Escherichia coli. Organism_taxid: 562. (4)

2a	1qppA01	A:1-121
2b	1qppB01	B:1-121

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: Pili_assembly_N (20)

Escherichia coli (8)

1a	Pili_assembly_N-1qppB01	B:1-121
1b	Pili_assembly_N-1qppB02	B:1-121

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

Family: Pili_assembly_C (20)

Escherichia coli (8)

2a	Pili_assembly_C-1qppB03	B:141-204
2b	Pili_assembly_C-1qppB04	B:141-204

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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).

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1qpp)

	Sites
(no "Sites" information available for 1qpp)

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

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	1qpp
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	PAPD_ECOLX \| P15319
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UniProtKB/Swiss-Prot
	PAPD_ECOLX \| P15319	:	1n0l 1pdk 1qpx 2j2z 2j7l 2uy6 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93

1qpx	PAPD CHAPERONE
3dpa	CHAPERONE PROTEIN PAPD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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