3JVV - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF P. AERUGINOSA PILT WITH BOUND AMP-PCP

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

Date :   17 Sep 09 (Deposition) - 02 Jun 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Hexameric P-Loop Atpase, Secretion Atpase, 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	:	PET23A
	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 (3, 7)

No.	Name	Count	Type	Full Name
1	ACP	3	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	CIT	1	Ligand/Ion	CITRIC ACID
3	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ACP	6	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	CIT	2	Ligand/Ion	CITRIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:131 , THR A:132 , GLY A:133 , SER A:134 , GLY A:135 , LYS A:136 , SER A:137 , THR A:138 , LEU A:268 , ARG A:276 , ALA A:278 , MG A:401	BINDING SITE FOR RESIDUE ACP A 400
2	AC2	SOFTWARE	SER A:137 , GLU A:163 , ACP A:400	BINDING SITE FOR RESIDUE MG A 401
3	AC3	SOFTWARE	TYR A:152 , LYS A:170 , ARG B:35 , ARG B:36 , TYR B:152 , LYS B:170 , ARG C:35 , ARG C:36	BINDING SITE FOR RESIDUE CIT A 357
4	AC4	SOFTWARE	ARG B:82 , THR B:132 , GLY B:133 , SER B:134 , GLY B:135 , LYS B:136 , SER B:137 , THR B:138 , LEU B:268 , ARG B:276 , ALA B:278 , HOH B:362 , MG B:401	BINDING SITE FOR RESIDUE ACP B 400
5	AC5	SOFTWARE	SER B:137 , GLU B:163 , HOH B:362 , ACP B:400	BINDING SITE FOR RESIDUE MG B 401
6	AC6	SOFTWARE	THR C:132 , GLY C:133 , SER C:134 , GLY C:135 , LYS C:136 , SER C:137 , THR C:138 , LEU C:268 , ARG C:276 , MG C:401	BINDING SITE FOR RESIDUE ACP C 400
7	AC7	SOFTWARE	SER C:137 , GLU C:163 , ACP C:400	BINDING SITE FOR RESIDUE MG C 401

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

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 3JVV)

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 3JVV)

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:331
 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.....eeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeee..eeeeeeeee............hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee............eeeeee......hhhhhhhhhh.....eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhheeeeeeeeee..----.eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.-------hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvv A   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKK----RVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKG-------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       310       320 |     330       340  
                                                                                                                                                                                                                                                                                                        271  276                                           322     330

Chain B from PDB  Type:PROTEIN  Length:328
 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.....eeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeee..eeeeeeee.............hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee............eeeeee......hhhhhhhhhh.....eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhheeeeeeee.-------...eeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhh.-------hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvv B   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTL-------RVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKG-------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       | -     | 280       290       300       310       320 |     330       340  
                                                                                                                                                                                                                                                                                                     268     276                                           322     330

Chain C 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 (1) --T2SE-3jvvC01 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --T2SE-3jvvC02 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --T2SE-3jvvC03 C:3-271                                                                                                                                                                                                                                                         ----------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhh...eeeee.....eeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeee..eeeeeeeee............hhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee............eeeeee......hhhhhhhhhh.....eeee....hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhheeeeeeeeeee.....eeeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhh.-----..hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T2SP_E         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvv C   1 MDITELLAFSAKQGASDLHLSAGLPPMIRVDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQNRGAGAVFRTIPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVGEMRDLETIRLALTAAETGHLVFGTLHTTSAAKTIDRVVDVFPAEEKAMVRSMLSESLQSVISQTLIKKIGGGRVAAHEIMIGTPAIRNLIREDKVAQMYSAIQTGGSLGMQTLDMCLKG-----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  
                                                                                                                                                                                                                                                                                                                                                           322   328

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 3JVV)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: T2SE (6)

Pseudomonas aeruginosa (2)

1a	T2SE-3jvvC01	C:3-271
1b	T2SE-3jvvC02	C:3-271
1c	T2SE-3jvvC03	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
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	Sites
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ 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
	3jvv
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	PILT_PSEAE \| P24559
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/Swiss-Prot
	PILT_PSEAE \| P24559	:	3jvu

2ewv	A. AEOLICUS PILT + ADP
2eww	A. AEOLICUS PILT + ATP
2gsz	A. AEOLICUS PILT HEXAMER
3jvu	P. AERUGINOSA PILT UNLIGANDED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (7, 7)

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