3C01 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURAL OF NATIVE SPAS C-TERMINAL DOMAIN

Authors :   R. Zarivach, W. Deng, M. Vuckovic, H. B. Felise, H. V. Nguyen, S. I. Mille B. B. Finlay, N. C. J. Strynadka

Date :   18 Jan 08 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E,F  (1x)
Biol. Unit 2: B,F,G  (1x)
Biol. Unit 3: C,E,G  (1x)
Biol. Unit 4: D,H  (1x)

Keywords :   Auto Cleavage Protein, Flagella, Escu, Yscu, Intein, T3Ss, Membrane, Inner Membrane, Transmembrane, Virulence, Membrane Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zarivach, W. Deng, M. Vuckovic, H. B. Felise, H. V. Nguyen, S. I. Miller, B. B. Finlay, N. C. Strynadka
Structural Analysis Of The Essential Self-Cleaving Type Iii Secretion Proteins Escu And Spas.
Nature V. 453 124 2008
PubMed-ID: 18451864 | Reference-DOI: 10.1038/NATURE06832

Molecule 1 - SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 211-258
	Gene	:	SPAS
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Strain	:	EPEC E2348/69

Molecule 2 - SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS
	Chains	:	E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 259-356
	Gene	:	SPAS
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Strain	:	EPEC E2348/69

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A				E	F
Biological Unit 2 (1x)	:		B				F	G
Biological Unit 3 (1x)	:			C		E		G
Biological Unit 4 (1x)	:				D				H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CYS	4	Ligand/Ion	CYSTEINE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CYS	2	Ligand/Ion	CYSTEINE
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	CYS	2	Ligand/Ion	CYSTEINE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	CYS	2	Ligand/Ion	CYSTEINE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	CYS	1	Ligand/Ion	CYSTEINE
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:246 , TYR E:293 , LYS E:296	BINDING SITE FOR RESIDUE SO4 E 66
02	AC2	SOFTWARE	ARG F:317	BINDING SITE FOR RESIDUE SO4 F 67
03	AC3	SOFTWARE	ARG G:317	BINDING SITE FOR RESIDUE SO4 G 68
04	AC4	SOFTWARE	HOH H:49 , ARG H:316 , ARG H:317	BINDING SITE FOR RESIDUE SO4 H 64
05	AC5	SOFTWARE	ARG H:317 , TYR H:318	BINDING SITE FOR RESIDUE SO4 H 69
06	AC6	SOFTWARE	ASP B:248 , VAL E:301 , ILE E:302 , VAL E:303 , TYR F:267 , MET F:277	BINDING SITE FOR RESIDUE CYS E 61
07	AC7	SOFTWARE	ASP A:248 , MET E:277 , ILE F:302 , VAL F:303	BINDING SITE FOR RESIDUE CYS F 62
08	AC8	SOFTWARE	ASP D:248 , ILE G:302 , VAL G:303 , TYR H:267	BINDING SITE FOR RESIDUE CYS G 60
09	AC9	SOFTWARE	ASP C:248 , ASN C:251 , TYR G:267 , MET G:277 , ILE H:302 , VAL H:303	BINDING SITE FOR RESIDUE CYS H 63
10	BC1	SOFTWARE	TYR G:318 , ASP H:304 , LEU H:332	BINDING SITE FOR RESIDUE MPD G 65

(no "SS Bond" information available for 3C01)

Asymmetric Unit

No.	Residues
1	Leu B:241	-	Ser B:242
2	Ala F:342	-	Gly F:343

(no "SAP(SNP)/Variant" information available for 3C01)

(no "PROSITE Motif" information available for 3C01)

(no "Exon" information available for 3C01)

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:20
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:20
                                   248       258
           SPAS_SALTY   239 EILSEQVKSDIENSRLIVAN 258
               SCOP domains d3c01.1              SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 3c01 A 239 EILSEQVKSDIENSRLIVAN 258
                                   248       258

Chain B from PDB  Type:PROTEIN  Length:20
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:20
                                   248       258
           SPAS_SALTY   239 EILSEQVKSDIENSRLIVAN 258
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 3c01 B 239 EILSEQVKSDIENSRLIVAN 258
                                   248       258

Chain C from PDB  Type:PROTEIN  Length:19
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:19
                                   249         
           SPAS_SALTY   240 ILSEQVKSDIENSRLIVAN 258
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 3c01 C 240 ILSEQVKSDIENSRLIVAN 258
                                   249

Chain D from PDB  Type:PROTEIN  Length:19
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:19
                                   249         
           SPAS_SALTY   240 ILSEQVKSDIENSRLIVAN 258
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 3c01 D 240 ILSEQVKSDIENSRLIVAN 258
                                   249

Chain E from PDB  Type:PROTEIN  Length:88
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:88
                                   268       278       288       298       308       318       328       338        
           SPAS_SALTY   259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKDV 346
               SCOP domains d3c01.1 A:239-258,E:259-346 Surface presentation of antigens protein SpaS                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeehhhhhhhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3c01 E 259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKDV 346
                                   268       278       288       298       308       318       328       338

Chain F from PDB  Type:PROTEIN  Length:87
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:87
                                   268       278       288       298       308       318       328       338       
           SPAS_SALTY   259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeeeeeehhhhhhhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3c01 F 259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
                                   268       278       288       298       308       318       328       338

Chain G from PDB  Type:PROTEIN  Length:87
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:87
                                   268       278       288       298       308       318       328       338       
           SPAS_SALTY   259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeehhhhhhhhhhhhhhh..eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3c01 G 259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
                                   268       278       288       298       308       318       328       338

Chain H from PDB  Type:PROTEIN  Length:87
 aligned with SPAS_SALTY | P40702 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:87
                                   268       278       288       298       308       318       328       338       
           SPAS_SALTY   259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeehhhhhhhhhhhhhhh..eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3c01 H 259 PTHITIGIYFKPELMPIPMISVYETNQRALAVRAYAEKVGVPVIVDIKLARSLFKTHRRYDLVSLEEIDEVLRLLVWLEEVENAGKD 345
                                   268       278       288       298       308       318       328       338

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: EscU C-terminal domain-like (15)

Superfamily: EscU C-terminal domain-like (15)

Family: EscU C-terminal domain-like (11)

Protein domain: Surface presentation of antigens protein SpaS (2)

Salmonella typhimurium [TaxId: 90371] (1)

d3c01.1

A:239-258,E:259-346

(no "CATH Domain" information available for 3C01)

(no "Pfam Domain" information available for 3C01)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (SPAS_SALTY | P40702)

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:0009306	protein secretion	The controlled release of proteins from a cell.
cellular component
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CYS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala F:342 - Gly F:343	[ RasMol ]
		Leu B:241 - Ser B:242	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3c01
		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
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SPAS_SALTY \| P40702
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SPAS_SALTY \| P40702
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3C01)

3bzl	CRYSTAL STRUCTURAL OF NATIVE ESCU C-TERMINAL DOMAIN
3bzo	CRYSTAL STRUCTURAL OF NATIVE ESCU C-TERMINAL DOMAIN WITH SPACE GROUP I 2 2 2
3bzp	CRYSTAL STRUCTURAL OF THE MUTATED N262A ESCU C-TERMINAL DOMAIN
3bzr	CRYSTAL STRUCTURAL OF THE MUTATED N262D ESCU C-TERMINAL DOMAIN
3bzs	CRYSTAL STRUCTURAL OF THE MUTATED N262D ESCU C-TERMINAL DOMAIN
3bzt	CRYSTAL STRUCTURAL OF THE MUTATED P263A ESCU C-TERMINAL DOMAIN
3bzv	CRYSTAL STRUCTURAL OF THE MUTATED T264A ESCU C-TERMINAL DOMAIN
3bzx	CRYSTAL STRUCTURAL OF THE MUTATED H265A ESCU C-TERMINAL DOMAIN
3bzy	CRYSTAL STRUCTURAL OF THE MUTATED Y316D ESCU C-TERMINAL DOMAIN
3bzz	CRYSTAL STRUCTURAL OF THE MUTATED R313T ESCU C-TERMINAL DOMAIN
3c00	CRYSTAL STRUCTURAL OF THE MUTATED G247T ESCU C-TERMINAL DOMAIN
3c03	CRYSTAL STRUCTURAL OF THE MUTATED P263A ESCU C-TERMINAL DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File