1M4V - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SET3, A SUPERANTIGEN-LIKE PROTEIN FROM STAPHYLOCOCCUS AUREUS

Authors :   V. L. Arcus, R. Langley, T. Proft, J. D. Fraser, E. N. Baker

Date :   05 Jul 02 (Deposition) - 17 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ob-Fold, Beta-Grasp, Superantigen Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. L. Arcus, R. Langley, T. Proft, J. D. Fraser, E. N. Baker
The Three-Dimensional Structure Of A Superantigen-Like Protein, Set3, From A Pathogenicity Island Of The Staphylococcus Aureus Genome
J. Biol. Chem. V. 277 32274 2002
PubMed-ID: 12082105 | Reference-DOI: 10.1074/JBC.M203914200
(for further references see the PDB file header)

Molecule 1 - SET3, SUPERANTIGEN-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A_3C
	Expression System Strain	:	AD494
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SET3
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	EXOTOXIN-LIKE PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1M4V)

(no "Site" information available for 1M4V)

(no "SS Bond" information available for 1M4V)

(no "Cis Peptide Bond" information available for 1M4V)

(no "SAP(SNP)/Variant" information available for 1M4V)

(no "PROSITE Motif" information available for 1M4V)

(no "Exon" information available for 1M4V)

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:196
 aligned with Q9ZFS6_STAAU | Q9ZFS6 from UniProtKB/TrEMBL  Length:234

    Alignment length:200
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
         Q9ZFS6_STAAU    35 SKYENVTKDIFDLRDYYSRASKELKNVTGYRYSKGGKHYLIFDKNRKFTRIQIFGKDIERIKKRKNPGLDIFVVKEAENRNGTVYSYGGVTKKNQGAYYDYLSAPRFVIKKEVGAGVSVHVKRYYIYKEEISLKELDFKLRQYLIQDFDLYKKFPKASKIKVTMKDGGYYTFELNKKLQTNRMSDVIDGRNIEKIEANIR 234
               SCOP domains d1m4va1 A:5-100 Superantigen-like protein SET3                                                  d1m4va2 A:101-204 Superantigen-like protein SET3                                                         SCOP domains
               CATH domains 1m4vA01           1m4vA02 A:23-97  [code=2.40.50.110, no name defined]                       1m4vA01 A:5-22,A:98-204  [code=3.10.20.120, no name defined]                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...eeeeeeeeeeeee..eeeeeeee..eeeeeee..hhhhhh...eeeeeeeee.....----.eeee..eee.............eeeeeeee..eeeeeeee......eeehhhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh..eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4v A   5 AKYENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDKHQKFTRIQIFGKDIERLKTRKNPGLDIFVVKEAE----TVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR 204
                                    14        24        34        44        54        64        74       | -  |     94       104       114       124       134       144       154       164       174       184       194       204
                                                                                                        82   87

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Q9ZFS6_STAAU | Q9ZFS6 from UniProtKB/TrEMBL  Length:234

    Alignment length:200
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
         Q9ZFS6_STAAU    35 SKYENVTKDIFDLRDYYSRASKELKNVTGYRYSKGGKHYLIFDKNRKFTRIQIFGKDIERIKKRKNPGLDIFVVKEAENRNGTVYSYGGVTKKNQGAYYDYLSAPRFVIKKEVGAGVSVHVKRYYIYKEEISLKELDFKLRQYLIQDFDLYKKFPKASKIKVTMKDGGYYTFELNKKLQTNRMSDVIDGRNIEKIEANIR 234
               SCOP domains d1m4vb1 B:5-100 Superantigen-like protein SET3                                                  d1m4vb2 B:101-204 Superantigen-like protein SET3                                                         SCOP domains
               CATH domains 1m4vB01           1m4vB02 B:23-97  [code=2.40.50.110, no name defined]                       1m4vB01 B:5-22,B:98-204  [code=3.10.20.120, no name defined]                                                CATH domains
           Pfam domains (1) ----------DUF1954-1m4vB03 B:15-98                                                             ------------Stap_Strp_tox_C-1m4vB01 B:111-204                                                              Pfam domains (1)
           Pfam domains (2) ----------DUF1954-1m4vB04 B:15-98                                                             ------------Stap_Strp_tox_C-1m4vB02 B:111-204                                                              Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhh...eeeeeeeeeeeee..eeeeeeee..eeeeeee.hhhhhhh...eeeeeeeee......---.eeee..eee.............eeeeeeee..eeeeeeee......eeehhhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh..eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4v B   5 AKYENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDKHQKFTRIQIFGKDIERLKTRKNPGLDIFVVKEAEN---TVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR 204
                                    14        24        34        44        54        64        74        |-  |     94       104       114       124       134       144       154       164       174       184       194       204
                                                                                                         83  87

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.120, no name defined] (91)

Staphylococcus aureus. Organism_taxid: 1280. (4)

1a	1m4vA01	A:5-22,A:98-204
1b	1m4vB01	B:5-22,B:98-204

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.110, no name defined] (136)

Staphylococcus aureus. Organism_taxid: 1280. (4)

2a	1m4vB02	B:23-97
2b	1m4vA02	A:23-97

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Staphylococcus aureus (41)

1a	Stap_Strp_tox_C-1m4vB01	B:111-204
1b	Stap_Strp_tox_C-1m4vB02	B:111-204

Clan: no clan defined [family: DUF1954] (9)

Family: DUF1954 (9)

Staphylococcus aureus (8)

2a	DUF1954-1m4vB03	B:15-98
2b	DUF1954-1m4vB04	B:15-98

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9ZFS6_STAAU | Q9ZFS6)

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.

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