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Title :   VIBRIO PARAHAEMOLYTICUS VTRA/VTRC COMPLEX BOUND TO THE BILE SALT TAURODEOXYCHOLATE

Authors :   D. R. Tomchick, K. Orth, G. Rivera-Cancel

Date :   10 Jun 16 (Deposition) - 20 Jul 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Heterodimer, Alpha/Beta, Calycin Beta Barrel Superfamily, Bile Salt Receptor, Taurodeoxycholate, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Li, G. Rivera-Cancel, L. N. Kinch, D. Salomon, D. R. Tomchick, N. V. Grishin, K. Orth
Bile Salt Receptor Complex Activates A Pathogenic Type Iii Secretion System.
Elife V. 5 2016
PubMed-ID: 27377244 | Reference-DOI: 10.7554/ELIFE.15718

Molecule 1 - VTRA PROTEIN
	Chains	:	A, C, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PACYCDUET1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	VTRA C-TERMINAL PERIPLASMIC DOMAIN, UNP RESIDUES 161-253
	Gene	:	VPA1332
	Organism Taxid	:	223926
	Strain	:	RIMD 2210633

Molecule 2 - VTRC PROTEIN
	Chains	:	B, D, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PACYCDUET1
	Fragment	:	VTRC C-TERMINAL PERIPLASMIC DOMAIN, UNP RESIDUES 31-161
	Gene	:	VPA1333
	Organism Taxid	:	223926
	Strain	:	RIMD 2210633

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	6SB	4	Ligand/Ion	TAURODEOXYCHOLATE
2	ACT	2	Ligand/Ion	ACETATE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	6SB	2	Ligand/Ion	TAURODEOXYCHOLATE
2	ACT	2	Ligand/Ion	ACETATE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	6SB	1	Ligand/Ion	TAURODEOXYCHOLATE
2	ACT	-1	Ligand/Ion	ACETATE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	6SB	1	Ligand/Ion	TAURODEOXYCHOLATE
2	ACT	-1	Ligand/Ion	ACETATE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:183 , HIS A:242 , GLU A:245 , TYR A:246 , ASN A:249 , HOH A:417	binding site for residue 6SB A 301
02	AC2	SOFTWARE	ARG A:230 , HOH A:422 , LYS B:40	binding site for residue ACT A 302
03	AC3	SOFTWARE	LEU A:185 , ASN A:212 , THR A:234 , LYS A:237 , LEU A:238	binding site for residue EDO A 303
04	AC4	SOFTWARE	TYR B:39 , TYR B:48 , HIS B:50 , ILE B:69 , GLU B:71 , TYR B:81 , PRO B:121 , SER B:123 , ILE B:124 , PHE B:150 , TYR B:151 , HOH B:422	binding site for residue 6SB B 301
05	AC5	SOFTWARE	LYS A:241 , ARG B:70 , LYS B:78 , TYR B:80 , ACT B:303	binding site for residue SO4 B 302
06	AC6	SOFTWARE	TYR A:240 , ARG B:70 , SO4 B:302	binding site for residue ACT B 303
07	AC7	SOFTWARE	SER C:181 , ASP C:182 , PHE C:183 , GLN C:184 , LYS F:59	binding site for residue SO4 C 302
08	AC8	SOFTWARE	LYS C:228 , ARG C:230 , HOH C:411 , LYS D:40	binding site for residue SO4 C 303
09	AC9	SOFTWARE	TYR D:39 , TYR D:81 , TYR D:118 , TYR D:151 , HOH D:402 , HOH D:403 , LYS E:200 , GLU E:245 , ASN E:249 , GLU E:252 , TYR E:253	binding site for residue 6SB D 301
10	AD1	SOFTWARE	LYS B:59 , HIS B:62 , ASP D:102 , ASN D:103 , HOH D:424	binding site for residue SO4 D 302
11	AD2	SOFTWARE	LYS C:214 , LYS E:228 , ARG E:230	binding site for residue SO4 E 302
12	AD3	SOFTWARE	TYR F:39 , TYR F:48 , GLU F:71 , TYR F:81 , SER F:123 , PHE F:150 , TYR F:151 , HOH F:406 , HOH F:413	binding site for residue 6SB F 301

(no "SS Bond" information available for 5KEW)

(no "Cis Peptide Bond" information available for 5KEW)

(no "SAP(SNP)/Variant" information available for 5KEW)

(no "PROSITE Motif" information available for 5KEW)

(no "Exon" information available for 5KEW)

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:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeee..hhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5kew A 165 DYPSLSFQQDYVYIFSSDFQLSEELGVALINALSAKEIVPERLYVMLNDKTISFSFISKNKKSKNRVLSTEKKLNYKHISEYIVNEIEY 253
                                   174       184       194       204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeeeeee....eeeeeeeeeeeeee......eee..hhhhhh....eeeeeeeee...eeeeee.hhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kew B   0 DPVHFYETSYKYQAADSTYMHDVAINVSIKGNHFTSDIIIRELVKSENKNYYNVIGHGDIIQKNTHQYYLNFDNIDVYTGTNKANMKPYKEPTSISSLINKSNNIRVVYLSEEYVVVEFFFYDGQIITLHRY 161
                            ||      39        49        59        69        79        89        99       109       119       129       139       149       159  
                            0|                                                                                                                                  
                            31

Chain C from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..eeee..hhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5kew C 164 DDYPSLSFQQDYVYIFSSDFQLSEELGVALINALSAKEIVPERLYVMLNDKTISFSFISKNKKSKNRVLSTEKKLNYKHISEYIVNEIEY 253
                                   173       183       193       203       213       223       233       243       253

Chain D from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee......eeeeeeeeeee..eeeeeeeeeee....eeeeeeeeeeeeeee....eeeeeeeeeeeeee......ee..hhhhh.eeeeeeee...eeeeeehhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kew D  31 PVHFYETSYKYQAADSTYMHDVAINVSIKGNHFTSDIIIRELVKSENKNYYNVIGHGDIIQKNTHQYYLNFDNIDVYTGTNKANMKPYSSLINKSNNIRVVYLSEEYVVVEFFFYDGQIITLHRY 161
                                    40        50        60        70        80        90       100       110       126       136       146       156     
                                                                                                                 118|                                    
                                                                                                                  125

Chain E from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeee.hhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeeee.....eeeeeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5kew E 166 YPSLSFQQDYVYIFSSDFQLSEELGVALINALSAKEIVPERLYVMLNDKTISFSFISKNKKSKNRVLSTEKKLNYKHISEYIVNEIEY 253
                                   175       185       195       205       215       225       235       245

Chain F from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeee...eeeeeeeeeeee....eeeeeeeeeeeeee.hhhhhee...hhhhhhhhhh.eeeeeeee...eeeeeehhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kew F  31 PVHFYETSYKYQAADSTYMHDVAINVSIKGNHFTSDIIIRELVKNYYNVIGHGDIIQKNTHQYYLNFDNIDVYTGTNKANMKPYKEPTSISSLINKSNNIRVVYLSEEYVVVEFFFYDGQIITLHRY 161
                                    40        50        60        70  ||    84        94       104       114       124       134       144       154       
                                                                     73|                                                                                   
                                                                      78

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	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 5KEW)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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