3LT6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   A TRANSITION FROM STRONG RIGHT-HANDED TO CANONICAL LEFT-HANDED SUPERCOILING IN A CONSERVED COILED COIL SEGMENT OF TRIMERIC AUTOTRANSPORTER ADHESINS - THE MUTANT 4 STRUCTURE

Authors :   K. Zeth, B. Hernandez-Alvarez, A. N. Lupas

Date :   15 Feb 10 (Deposition) - 31 Mar 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Yada, Trimeric Autotransporter, Core Residues, Cell Adhesion, Cell Membrane, Cell Outer Membrane, Membrane, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. H. Alvarez, M. Gruber, A. Ursinus, S. Dunin-Horkawicz, A. N. Lupas, K. Zeth
A Transition From Strong Right-Handed To Canonical Left-Handed Supercoiling In A Conserved Coiled-Coil Segment Of Trimeric Autotransporter Adhesins.
J. Struct. Biol. V. 170 236 2010
PubMed-ID: 20178846 | Reference-DOI: 10.1016/J.JSB.2010.02.009

Molecule 1 - ADHESIN YADA
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRIMERIC COILED COIL
	Gene	:	YADA, INVA, YOP1, YOPA
	Organism Scientific	:	YERSINIA ENTEROCOLITICA
	Organism Taxid	:	630

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3LT6)

(no "SS Bond" information available for 3LT6)

Asymmetric Unit

No.	Residues
1	Lys A:-7	-	Ser A:-6
2	Asn C:53	-	Ser C:54

(no "SAP(SNP)/Variant" information available for 3LT6)

(no "PROSITE Motif" information available for 3LT6)

(no "Exon" information available for 3LT6)

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:54
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:54
                                   342       352       362       372       382    
          YADA1_YEREN   333 KSSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGL 386
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3lt6 A  -7 KSSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLL  46
                                     2        12        22     |  32        42    
                                                              28-MSE

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:61
                                   345       355       365       375       385       395 
          YADA1_YEREN   336 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLF 396
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 3lt6 B  -4 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLLASSAALNSLF  56
                                     5        15        25  |     35        45        55 
                                                           28-MSE

Chain C from PDB  Type:PROTEIN  Length:59
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:59
                                   345       355       365       375       385         
          YADA1_YEREN   336 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNS 394
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 3lt6 C  -4 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLLASSAALNS  54
                                     5        15        25  |     35        45         
                                                           28-MSE

Chain D from PDB  Type:PROTEIN  Length:62
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:62
                                   344       354       364       374       384       394  
          YADA1_YEREN   335 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLF 396
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 3lt6 D  -5 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLLASSAALNSLF  56
                                     4        14        24   |    34        44        54  
                                                            28-MSE

Chain E from PDB  Type:PROTEIN  Length:57
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:57
                                   342       352       362       372       382       
          YADA1_YEREN   333 KSSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASS 389
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 3lt6 E  -7 KSSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLLASS  49
                                     2        12        22     |  32        42       
                                                              28-MSE

Chain F from PDB  Type:PROTEIN  Length:63
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:63
                                   343       353       363       373       383       393   
          YADA1_YEREN   334 SSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFRQLDNRLDKLDTRVDKGLASSAALNSLF 396
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------YadA-3lt6F01        Pfam domains (1)
           Pfam domains (2) --------------------------------------------YadA-3lt6F02        Pfam domains (2)
           Pfam domains (3) --------------------------------------------YadA-3lt6F03        Pfam domains (3)
           Pfam domains (4) --------------------------------------------YadA-3lt6F04        Pfam domains (4)
           Pfam domains (5) --------------------------------------------YadA-3lt6F05        Pfam domains (5)
           Pfam domains (6) --------------------------------------------YadA-3lt6F06        Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 3lt6 F  -6 SSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKmHQLENRLDKLEKRLLKLLASSAALNSLF  56
                                     3        13        23    |   33        43        53   
                                                             28-MSE

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 3LT6)

(no "CATH Domain" information available for 3LT6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Pilus (9)

Family: YadA (2)

Yersinia enterocolitica (2)

1a	YadA-3lt6F01	F:38-56
1b	YadA-3lt6F02	F:38-56
1c	YadA-3lt6F03	F:38-56
1d	YadA-3lt6F04	F:38-56
1e	YadA-3lt6F05	F:38-56
1f	YadA-3lt6F06	F:38-56

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (YADA1_YEREN | P31489)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

Asymmetric Unit
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	Sites
(no "Sites" information available for 3lt6)

	Cis Peptide Bonds
		Asn C:53 - Ser C:54	[ RasMol ]
		Lys A:-7 - Ser A:-6	[ RasMol ]

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

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Access by PDB/NDB ID
	3lt6
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Access by UniProt ID/Accession number
	YADA1_YEREN \| P31489
		Comparative Protein Structure Models	:	ModBase
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	YADA1_YEREN \| P31489
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UniProtKB/Swiss-Prot
	YADA1_YEREN \| P31489	:	1p9h 3lt7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

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

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SCOP Domains (0, 0)

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Pfam Domains (1, 6)

Gene Ontology (7, 7)

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