2J0N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   A PROTEOLYTICALLY TRUNCATED FORM OF SHIGELLA FLEXNERI IPAD

Authors :   S. Johnson, P. Roversi, S. M. Lea

Date :   03 Aug 06 (Deposition) - 02 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Ipad, T3Ss, Plasmid, Virulence, Shigella Flexneri, Type Iii Secretion, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Johnson, P. Roversi, M. Espina, A. Olive, J. E. Deane, S. Birket, T. Field, W. D. Picking, A. J. Blocker, E. E. Galyov, W. L. Picking, S. M. Lea
Self-Chaperoning Of The Type Iii Secretion System Needle Tip Proteins Ipad And Bipd.
J. Biol. Chem. V. 282 4035 2007
PubMed-ID: 17077085 | Reference-DOI: 10.1074/JBC.M607945200
(for further references see the PDB file header)

Molecule 1 - INVASIN IPAD
	Atcc	:	700930
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	DE3
	Fragment	:	TRUNCATED FORM, RESIDUES 133-332
	Organism Common	:	SHIGELLA
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Other Details	:	THE TRUNCATION WAS OBTAINED BY IN-DROP CLEAVAGE BY UNKOWN PROTEASE OF A CONSTRUCT CONSISTING OF RESIDUES 15-332
	Strain	:	301
	Synonym	:	IPAD
	Variant	:	SEROTYPE 2A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2J0N)

(no "Site" information available for 2J0N)

(no "SS Bond" information available for 2J0N)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:182	-	Asn A:183
2	Tyr A:212	-	Pro A:213
3	Asp B:184	-	Gly B:185
4	Tyr B:212	-	Pro B:213
5	Leu B:263	-	Gly B:264

Asymmetric/Biological Unit (7, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_IPAD_SHIFL_003 *	A	136	D	IPAD_SHIFL	---	---	B	A	136	D
2	UniProt	VAR_IPAD_SHIFL_004 *	N	140	K	IPAD_SHIFL	---	---	B	N	140	K
3	UniProt	VAR_IPAD_SHIFL_005 *	D	144	N	IPAD_SHIFL	---	---	A/B	D	144	N
4	UniProt	VAR_IPAD_SHIFL_006 *	N	193	K	IPAD_SHIFL	---	---	A/B	N	193	K
5	UniProt	VAR_IPAD_SHIFL_007 *	Q	220	K	IPAD_SHIFL	---	---	A/B	Q	220	K
6	UniProt	VAR_IPAD_SHIFL_008 *	Q	239	E	IPAD_SHIFL	---	---	A/B	Q	239	E
7	UniProt	VAR_IPAD_SHIFL_009 *	S	247	N	IPAD_SHIFL	---	---	A/B	S	247	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2J0N)

(no "Exon" information available for 2J0N)

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
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Chain A from PDB  Type:PROTEIN  Length:171
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:171
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
           IPAD_SHIFL   144 DINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKV 314
               SCOP domains d2j0na1 A:144-314 Invasin IpaD                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeehhhhhhhhhhhhhhhh...........hhhhhhhhhhhh....eeeeee..eeeeee.hhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j0n A 144 DINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKV 314
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

Chain B from PDB  Type:PROTEIN  Length:187
 aligned with IPAD_SHIFL | P18013 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:187
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       
           IPAD_SHIFL   133 ELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTI 319
               SCOP domains d2j0nb_ B: Invasin IpaD                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeehhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---D---K---N------------------------------------------------K--------------------------K------------------E-------N------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j0n B 133 ELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTI 319
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: IpaD-like (12)

Superfamily: IpaD-like (12)

Family: IpaD-like (10)

Protein domain: Invasin IpaD (3)

Shigella flexneri [TaxId: 623] (3)

1a	d2j0na1	A:144-314
1b	d2j0nb_	B:

(no "CATH Domain" information available for 2J0N)

(no "Pfam Domain" information available for 2J0N)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IPAD_SHIFL | P18013)

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 2j0n)

	Cis Peptide Bonds
		Asp B:184 - Gly B:185	[ RasMol ]
		Gly A:182 - Asn A:183	[ RasMol ]
		Leu B:263 - Gly B:264	[ RasMol ]
		Tyr A:212 - Pro A:213	[ RasMol ]
		Tyr B:212 - Pro B:213	[ RasMol ]

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	2j0n
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	IPAD_SHIFL \| P18013
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	IPAD_SHIFL \| P18013	:	2j0o 2jaa 3r9v 4d3e

2j0o	SHIGELLA FLEXNERI IPAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 12)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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