2VQI - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE P PILUS USHER (PAPC) TRANSLOCATION PORE

Authors :   H. Remaut, C. Tang, N. S. Henderson, J. S. Pinkner, T. Wang, S. J. Hultgren, D. G. Thanassi, H. Li, G. Waksman

Date :   16 Mar 08 (Deposition) - 27 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B  (2x)

Keywords :   Transmembrane, Outer Membrane, Transport, Usher, P Pilus, Membrane, Fimbrium, Om Translocation Pore, Pilus Assembly Platform (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Remaut, C. Tang, N. S. Henderson, J. S. Pinkner, T. Wang, S. J. Hultgren, D. G. Thanassi, G. Waksman, H. Li
Fiber Formation Across The Bacterial Outer Membrane By The Chaperone/Usher Pathway.
Cell(Cambridge, Mass. ) V. 133 640 2008
PubMed-ID: 18485872 | Reference-DOI: 10.1016/J.CELL.2008.03.033

Molecule 1 - OUTER MEMBRANE USHER PROTEIN PAPC
	Atcc	:	700336
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834 (DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PMON6235
	Fragment	:	TRANSLOCATION DOMAIN, RESIDUES 157-667
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	J96
	Synonym	:	PAPC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	C8E	2	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	LDA	2	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 20)

No.	Name	Count	Type	Full Name
1	C8E	2	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	LDA	2	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	C8E	-1	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	LDA	2	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (3, 22)

No.	Name	Count	Type	Full Name
1	C8E	4	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	LDA	2	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU B:399 , LEU B:423 , ARG B:510 , LEU B:524	BINDING SITE FOR RESIDUE C8E B1637
2	AC2	SOFTWARE	ILE A:615 , LEU B:340 , LEU B:378	BINDING SITE FOR RESIDUE C8E B1638
3	AC3	SOFTWARE	PHE A:573 , TYR A:580 , LEU B:224 , LEU B:246 , SER B:342 , GLY B:343 , VAL B:356 , PHE B:357	BINDING SITE FOR RESIDUE LDA B1639
4	AC4	SOFTWARE	LEU A:340 , SER A:342 , GLY A:343 , VAL A:356 , PHE A:357 , PHE B:573 , TYR B:580	BINDING SITE FOR RESIDUE LDA A1638

(no "SS Bond" information available for 2VQI)

(no "Cis Peptide Bond" information available for 2VQI)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIMBRIAL_USHER	PS01151	Fimbrial biogenesis outer membrane usher protein signature.	PAPC_ECOLX	315-325	2	A:288-298 B:288-298

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIMBRIAL_USHER	PS01151	Fimbrial biogenesis outer membrane usher protein signature.	PAPC_ECOLX	315-325	2	A:288-298 B:288-298

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIMBRIAL_USHER	PS01151	Fimbrial biogenesis outer membrane usher protein signature.	PAPC_ECOLX	315-325	2	A:288-298 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIMBRIAL_USHER	PS01151	Fimbrial biogenesis outer membrane usher protein signature.	PAPC_ECOLX	315-325	2	- B:288-298

(no "Exon" information available for 2VQI)

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:477
 aligned with PAPC_ECOLX | P07110 from UniProtKB/Swiss-Prot  Length:836

    Alignment length:492
                                   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 LMLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGPWRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLESDDRMLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSMVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGYGHETEGPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKSWRLSYSKRFDNADADITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNVADWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVFGLQGVAVGLSASRSKYLGRDNDSAYLRISVPLGTGTASYSGSMSNDRYVNMAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGGATITG 664
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................................-.....................................................................---.................................................................................................----..............................................................................----.................................................................................-.........................................................................--.............................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------FIMBRIAL_US--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vqi A 146 LmLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNL-PWRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLES---mLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSmVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGY----EGPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKSWRLSYSKRFD----DITFAGYRFSERNYmTmEQYLNARYRNDYSSREKEmYTVTLNKNVADWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVF-LQGVAVGLSASRSKYLGRDNDSAYLRISVPLGTGTASYSGSmSNDRYVNmAGYTDTFNDGLDSYSLNAGLNSG--LTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGGATITG 637
                             |     155       165       175  | |  185       195       205       215       225       235       245  |   |255       265       275       285 |     295       305       315       325       335       345  |    355       365       375       385       395       405       415       425    |  435       445   | | 455       465    |  475       485       495       505       515 |     525       535       545       555  |    565|      575       585   |  |595       605       615       625       635  
                             |                            178 |                                                                 248   |                                287-MSE                                                      348  353                                                                          430  435           449-MSE              470-MSE                                      515 |                                      558-MSE 566-MSE                589  |                                             
                           147-MSE                          180                                                                     252-MSE                                                                                                                                                                                                451-MSE                                                           517                                                                        592

Chain B from PDB  Type:PROTEIN  Length:477
 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 (1) PapC_N-2vq-------------Usher-2vqiB01 B:169-636                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) PapC_N-2vq-------------Usher-2vqiB02 B:169-636                                                                                                                                                                                                                                                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author .......................................................................................................---..................................................................................................----............................................................................----..................................................................................---...................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------FIMBRIAL_US-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqi B 146 LmLDYNLNGTVSRNYQGGDSHQFSYNGTVGGNLGPWRLRADYQGSQEQSRYNGEKTTNRNFTWSRFYLFRAIPRWRANLTLGENNINSDIFRSWSYTGASLES---mLPPRLRGYAPQITGIAETNARVVVSQQGRVLYDSmVPAGPFSIQDLDSSVRGRLDVEVIEQNGRKKTFQVDTASVPYLTRPGQVRYKLVSGRSRGYG----GPVFATGEASWGLSNQWSLYGGAVLAGDYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKSWRLSYSKRF----ADITFAGYRFSERNYmTmEQYLNARYRNDYSSREKEmYTVTLNKNVADWNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNVF---GVAVGLSASRSKYLGRDNDSAYLRISVPLGTGTASYSGSmSNDRYVNmAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGGATIT 636
                             |     155       165       175       185       195       205       215       225       235       245  |   |255       265       275       285 |     295       305       315       325       335       345   |   355       365       375       385       395       405       415       425   |   435       445   | | 455       465    |  475       485       495       505       515   |   525       535       545       555  |    565|      575       585       595       605       615       625       635 
                           147-MSE                                                                                              248   |                                287-MSE                                                       349  354                                                                        429  434            449-MSE              470-MSE                                      515 519                                    558-MSE 566-MSE                                                                  
                                                                                                                                    252-MSE                                                                                                                                                                                                451-MSE

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 '\|'

(no "SCOP Domain" information available for 2VQI)

(no "CATH Domain" information available for 2VQI)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MBB (97)

Family: Usher (2)

Escherichia coli (1)

1a	Usher-2vqiB01	B:169-636
1b	Usher-2vqiB02	B:169-636

Clan: no clan defined [family: PapC_N] (4)

Family: PapC_N (4)

Escherichia coli (1)

2a	PapC_N-2vqiB03	B:146-155
2b	PapC_N-2vqiB04	B:146-155

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.

Asymmetric Unit
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	2vqi
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	PAPC_ECOLX \| P07110
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	PAPC_ECOLX \| P07110	:	2kt6 3fip

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Description

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Ligands, Modified Residues, Ions (3, 20)

Sites (4, 4)

SS Bonds (0, 0)

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