3ZQE - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PRGI-SIPD FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH DEOXYCHOLATE

Authors :   M. Lunelli, M. Kolbe

Date :   09 Jun 11 (Deposition) - 17 Aug 11 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

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

Keywords :   Cell Invasion, Cell Invasion Complex, Type Iii Secretion, T3Ss, Tip Complex, Host Pathogen Interaction, Bacterial Pathogenesis, Bile Salt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Lunelli, R. Hurwitz, J. Lambers, M. Kolbe
Crystal Structure Of Prgi-Sipd: Insight Into A Secretion Competent State Of The Type Three Secretion System Needle Tip And Its Interaction With Host Ligands
Plos Pathog. V. 7 02163 2011
PubMed-ID: 21829362 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002163

Molecule 1 - PROTEIN PRGI, CELL INVASION PROTEIN SIPD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	PRGI FUSED WITH SIPD RESIDUES 127-343
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	216597
	Other Details	:	GGSGG LINK INSERTED BETWEEN PRGI AND SIPD
	Strain	:	SL1344
	Synonym	:	SALMONELLA INVASION PROTEIN D, PRGI-SIPD FUSION PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	DXC	1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	DXC	-1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DXC	1	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
2	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:37 , SER A:39 , HOH A:2056 , LEU B:31 , TYR B:47 , TYR B:54	BINDING SITE FOR RESIDUE DXC B1079
2	AC2	SOFTWARE	LEU A:150 , TYR A:248 , GLY A:249 , ASN A:316 , TYR A:319 , ASP A:320 , GLN B:288	BINDING SITE FOR RESIDUE GOL A1337
3	AC3	SOFTWARE	ASN A:300 , THR A:303 , THR A:304 , GLN B:310	BINDING SITE FOR RESIDUE GOL A1338

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

Asymmetric Unit

No.	Residues
1	Phe A:215	-	Pro A:216
2	Phe B:215	-	Pro B:216

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

(no "PROSITE Motif" information available for 3ZQE)

(no "Exon" information available for 3ZQE)

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:274
 aligned with PRGI_SALTY | P41784 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:274
                                                                                                                                           80                                                                                                                                                                 
                                                                                                   78                                     79|                                                                                                                                                                 
                                    15        25        35        45        55        65        75  |      -         -         -         - ||      -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -    
           PRGI_SALTY     6 SGYLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDIDAAIIQN--------------------------------------FR-----------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqe A   6 SGYLDDVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTVKVFKDIDAAIIQNISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
                                    15        25        35        45        55        65        75  ||   135       145       155       165       175  ||   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
                                                                                                   78|                                              178|                                                                                                                                                      
                                                                                                   129                                               186

Chain A from PDB  Type:PROTEIN  Length:274
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:324
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           SIPD_SALTY    13 PGIVAERPQTPSASEHVETAVVPSTTEHRGTDIISLSQAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh------hhhhhhhhhh---------------hhhhhhhhhhhhhhhh.------.hhhhhhhhhhhhhhhhhhhh-----hhhh----------hhhhhhhhhhhhh..-.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------.eeehhhhhhhhhhhhhhhhh......eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zqe A   6 SGYLDD------VSAKFDTGVD---------------NLQTQVTEALDKLAAKP------SDPALLAAYQSKLSEYNLYRN-----AQSN----------TVKVFKDIDAAIIQN-ISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWL-------TVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLET 336
                                 |   -  |     19 |       -       |24        34   |     -|       48        58|     | 63         -|       73    | |132       142       152       162       172     |   -   |   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
                                11     12       21              22              38     39                  59    60 63         64            78 |                                              178     186                                                                                                                                                      
                                                                                                                                              129

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with PRGI_SALTY | P41784 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:250
                                                                                                                                                       80                                                                                                                             
                                                                                64          65   70                         71     78                 79|                                                                                                                             
                                    20        30        40        50        60   |     -     |  69|        -         -       |73    |    -         -   ||    -         -         -         -         -         -         -         -         -         -         -         -         -
           PRGI_SALTY    11 DVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNT-----------VKVFKD--------------------------IDAAIIQN------------------FR-----------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.hhh.eeeehhhhhhhhhhhhhhhhhh.....eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqe B  11 DVSAKFDTGVDNLQTQVTEALDKLAAKPSDPALLAAYQSKLSEYNLYRNAQSNTGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFL 341
                                    20        30        40        50        60   ||  151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
                                                                                64|                                                                                                                                                                                                   
                                                                                146

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with SIPD_SALTY | Q56026 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:292
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
           SIPD_SALTY    50 QAATKIHQAQQTLQSTPPISEENNDERTLARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFL 341
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh-----------------hhhhhhhhhhhh-----------------..hhhhhhhh-----hhhhhhhhhhhhhhhh.---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.hhh.eeeehhhhhhhhhhhhhhhhhh.....eee...........hhhhhhhhhhhhh.hhh.eeee..eeeee..hhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zqe B  11 DVSAKFDTGVDNLQT-----------------QVTEALDKLAAK-----------------PSDPALLAAY-----QSKLSEYNLYRNAQSNT---GDSYLGVYENVVAVYTDFYQAFSDILSKMGGWLLPGKDGNTVKLDVTSLKNDLNSLVNKYNQINSNTVLFPAQSGSGVKVATEAEARQWLSELNLPNSCLKSYGSGYVVTVDLTPLQKMVQDIDGLGAPGKDSKLEMDNAKYQAWQSGFKAQEENMKTTLQTLTQKYSNANSLYDNLVKVLSSTISSSLETAKSFL 341
                                    20    |    -         -  |     33   |     -         - |      46|     | 51        61  |   |149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
                                         25                26         37                38       47    48              64 146

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 3ZQE)

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

(no "Pfam Domain" information available for 3ZQE)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SIPD_SALTY | Q56026)

biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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.

Chain A,B (PRGI_SALTY | P41784)

molecular function
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:215 - Pro A:216	[ RasMol ]
		Phe B:215 - Pro B:216	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	3zqe
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	PRGI_SALTY \| P41784
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SIPD_SALTY \| Q56026
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	PRGI_SALTY \| P41784
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	SIPD_SALTY \| Q56026
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PRGI_SALTY \| P41784	:	2jow 2kv7 2lpz 2mex 2x9c 3zqb
	SIPD_SALTY \| Q56026	:	2ym0 2ym9 3nzz 3o00 3o01 3o02 3zqb

2x9c	CRYSTAL STRUCTURE OF A SOLUBLE PRGI MUTANT FROM SALMONELLA TYPHIMURIUM
2ym0	TRUNCATED SIPD FROM SALMONELLA TYPHIMURIUM
2ym9	SIPD FROM SALMONELLA TYPHIMURIUM
3zqb	PRGI-SIPD FROM SALMONELLA TYPHIMURIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 6)

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