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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCAL EENTEROTOXIN B IN COMPLEX WITH A NOVEL NEUTRALIZATION MONOCLONAL ANTIBODY FAB FRAGMENT

Authors :   S. Y. Liang, S. Hu, J. X. Dai, Y. J. Guo, Z. Y. Lou

Date :   28 Nov 12 (Deposition) - 25 Dec 13 (Release) - 16 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,H,L

Keywords :   Staphylococcal Eenterotoxin B, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Xia, S. Liang, H. Wang, S. Hu, Y. Sun, X. Yu, J. Han, J. Li, S. Guo, J. Dai Z. Lou, Y. Guo
Structural Basis For The Neutralization And Specificity Of Staphylococcal Enterotoxin B Against Its Mhc Class Ii Binding Site.
Mabs V. 6 119 2014
PubMed-ID: 24423621 | Reference-DOI: 10.4161/MABS.27106

Molecule 1 - ENTEROTOXIN TYPE B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ENTB
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	SEB

Molecule 2 - MONOCLONAL ANTIBODY 3E2 FAB FIGMENT LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - MONOCLONAL ANTIBODY 3E2 FAB FIGMENT HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:99 , PHE H:51 , ALA H:52 , TYR H:72 , TYR H:119 , TYR H:124 , HOH H:415 , HOH H:422	BINDING SITE FOR RESIDUE SO4 H 301

Asymmetric/Biological Unit

No.	Residues
1	A:120	-	A:140
2	H:40	-	H:114
3	H:166	-	H:221
4	L:45	-	L:111
5	L:157	-	L:217

Asymmetric/Biological Unit

No.	Residues
1	Asp A:154	-	Lys A:155
2	Ser L:29	-	Pro L:30
3	Tyr L:117	-	Pro L:118
4	Tyr L:163	-	Pro L:164
5	Phe H:172	-	Pro H:173
6	Glu H:174	-	Pro H:175
7	Arg H:214	-	Pro H:215

(no "SAP(SNP)/Variant" information available for 3W2D)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	STAPH_STREP_TOXIN_1	PS00277	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1.	ETXB_STAAU	142-151	1	A:142-151
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ETXB_STAAU	179-202	1	A:179-202

(no "Exon" information available for 3W2D)

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
	(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:225
 aligned with ETXB_STAAU | P01552 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:237
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       
           ETXB_STAAU    29 SQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKK 265
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhh......eeeeee.........eeeee..---.....eeeee.....hhhhhh...eeeee..............---------.eeeee..eee..........eeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeee.........hhhhhhhhhhhh........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------STAPH_STRE---------------------------STAPH_STREP_TOXIN_2     --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2d A  29 SQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIK---LGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTN---------RKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKK 265
                                    38        48        58        68        78  |   | 88        98       108       118        |-       138       148       158       168       178       188       198       208       218       228       238       248       258       
                                                                               81  85                                       127       137

Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....ee.......eeeee..........eeeeee.....eeeeeee...........hhh.eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeee....eeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2d H  19 DVQLQESGPGLVRPSQSLSLTCTVTGYSLTSDFAWNWIRQFPGNKLEWMGYINYSGYTNYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREAYYGRAYWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC 241
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee........eee...hhhhhhh..eeeeeee..........eee............ee...........eeeeeeehhhhhh.....eeee........ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2d L  23 ENVLTQSPAIMSASPGETVTMTCRATSSVSSTYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYINYPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 237
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

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 3W2D)

(no "CATH Domain" information available for 3W2D)

(no "Pfam Domain" information available for 3W2D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ETXB_STAAU | P01552)

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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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg H:214 - Pro H:215	[ RasMol ]
		Asp A:154 - Lys A:155	[ RasMol ]
		Glu H:174 - Pro H:175	[ RasMol ]
		Phe H:172 - Pro H:173	[ RasMol ]
		Ser L:29 - Pro L:30	[ RasMol ]
		Tyr L:117 - Pro L:118	[ RasMol ]
		Tyr L:163 - Pro L:164	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (5, 5)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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