3JVU - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNLIGANDED P. AERUGINOSA PILT

Authors :   A. M. Misic, K. A. Satyshur, K. T. Forest

Date :   17 Sep 09 (Deposition) - 21 Jul 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Motor Protein, P-Loop Atpase, Type Iv Pili, Atp-Binding, Fimbrium, Nucleotide-Binding, Transport, Atp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Misic, K. A. Satyshur, K. T. Forest
P. Aeruginosa Pilt Structures With And Without Nucleotide Reveal A Dynamic Type Iv Pilus Retraction Motor.
J. Mol. Biol. V. 400 1011 2010
PubMed-ID: 20595000 | Reference-DOI: 10.1016/J.JMB.2010.05.066

Molecule 1 - TWITCHING MOBILITY PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PA0395, PILT
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PA103

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:133	BINDING SITE FOR RESIDUE CL A 400
2	AC2	SOFTWARE	TYR A:152 , ARG B:35 , ARG B:36 , TYR B:152 , LYS B:170 , HOH B:358 , ARG C:35 , ARG C:36	BINDING SITE FOR RESIDUE CIT B 357
3	AC3	SOFTWARE	GLY C:135	BINDING SITE FOR RESIDUE CL C 400

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

Asymmetric Unit

No.	Residues
1	Asp A:160	-	Pro A:161
2	Asp B:160	-	Pro B:161
3	Asp C:160	-	Pro C:161

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	T2SP_E	PS00662	Bacterial type II secretion system protein E signature.	PILT_PSEAE	193-207	3	A:193-207 B:193-207 C:193-207

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	T2SP_E	PS00662	Bacterial type II secretion system protein E signature.	PILT_PSEAE	193-207	6	A:193-207 B:193-207 C:193-207

(no "Exon" information available for 3JVU)

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:337
 aligned with PILT_PSEAE | P24559 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
           PILT_PSEAE     1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKIGGGRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKGLVAKGLISRENAREKAKIPE 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee..eeeeeee..eeee......hhhhhhhhhhh..hhhhhhhhhhhheeeeeeee...eeeeeeeeee..eeeeeeeee............hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhh....eeeeee............eeeeee......hhhhhhhhhh.....eeee....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee..---..eeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..--..hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvu A   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKK---GRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKGLVA--LISRENAREKAKIPE 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|   |  280       290       300       310       320    |  330       340  
                                                                                                                                                                                                                                                                                                        271 275                                               325  |              
                                                                                                                                                                                                                                                                                                                                                                 328

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with PILT_PSEAE | P24559 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
           PILT_PSEAE     1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKIGGGRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKG 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeee..eeeeeee..eeee......hhhhhhhhhhh..hhhhhhhhhhhheeeeeeee...eeeeeeeeee..eeeeeeee.......hhhhh.hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhh....eeeeee............eeeeee......hhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee...---.eeeeeeee.hhhhhhhh--..hhhhhhhhhhhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvu B   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKI---RVAAHEIMIGTPAIRNLI--DKVAQMYSAIQTGGSLGMQTLDMCLKG 322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 |   | 280       290  |  | 300       310       320  
                                                                                                                                                                                                                                                                                                         272 276              293  |                          
                                                                                                                                                                                                                                                                                                                                 296

Chain C from PDB  Type:PROTEIN  Length:334
 aligned with PILT_PSEAE | P24559 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
           PILT_PSEAE     1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKIGGGRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKGLVAKGLISRENAREKAKIPE 342
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --T2SE-3jvuC01 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --T2SE-3jvuC02 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --T2SE-3jvuC03 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhh...eeeee..eeeeeee..eeee......hhhhhhhhhhh..hhhhhhhhhhhheeeeeeee...eeeeeeeeee..eeeeeeee.............hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhh....eeeeee............eeeeee......hhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.....eeeeeeeee.hhhhhhhhhh..hhhhhhhhhh..--...hhhhhhhhh------hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvu C   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKIGGGRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGG--GMQTLDMCLKGL------SRENAREKAKIPE 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        |- |     320  |    330       340  
                                                                                                                                                                                                                                                                                                                                              309  |        323    330            
                                                                                                                                                                                                                                                                                                                                                 312

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 3JVU)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: T2SE (6)

Pseudomonas aeruginosa (2)

1a	T2SE-3jvuC01	C:3-271
1b	T2SE-3jvuC02	C:3-271
1c	T2SE-3jvuC03	C:3-271

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PILT_PSEAE | P24559)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0043108	pilus retraction	The process of withdrawing a pilus back into a cell.
	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.
	GO:0043107	type IV pilus-dependent motility	Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0044096	type IV pilus	A short filamentous structure on the surface of a bacterial cell distinguished from other pili by post-translational N-methylation of the pilin monomers.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:160 - Pro A:161	[ RasMol ]
		Asp B:160 - Pro B:161	[ RasMol ]
		Asp C:160 - Pro C:161	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3jvu
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	PILT_PSEAE \| P24559
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		Domain Information	:	XDom
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	PILT_PSEAE \| P24559
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UniProtKB/Swiss-Prot
	PILT_PSEAE \| P24559	:	3jvv

2ewv	A. AEOLICUS PILT WITH ADP
2eww	A. AEOLICUS PILT WITH ATP
2gsz	A. AEOLICUS PILT HEXAMER
3jvv	CRYSTAL STRUCTURE OF P. AERUGINOSA AMP-PCP BOUND PILT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File