1SBB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB

Authors :   H. Li, R. A. Mariuzza

Date :   22 Feb 99 (Deposition) - 01 Mar 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   T Cell Receptor, Superantigen, Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Li, A. Llera, D. Tsuchiya, L. Leder, X. Ysern, P. M. Schlievert, K. Karjalainen, R. A. Mariuzza
Three-Dimensional Structure Of The Complex Between A T Cell Receptor Beta Chain And The Superantigen Staphylococcal Enterotoxin B.
Immunity V. 9 807 1998
PubMed-ID: 9881971 | Reference-DOI: 10.1016/S1074-7613(00)80646-9
(for further references see the PDB file header)

Molecule 1 - PROTEIN (14.3.D T CELL ANTIGEN RECEPTOR)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	BETA CHAIN
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN B)
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	RN9220
	Synonym	:	SEB

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1SBB)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:92
2	A:147	-	A:212
3	B:93	-	B:113
4	C:23	-	C:92
5	C:147	-	C:212
6	D:93	-	D:113

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Phe A:153	-	Pro A:154
3	Ser C:7	-	Pro C:8
4	Phe C:153	-	Pro C:154

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TCB1_MOUSE_001 *	Y	70	H	TCB1_MOUSE	---	---	A/C	Y	190	H
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 4)

	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	2	B:115-124 D:115-124
2	STAPH_STREP_TOXIN_2	PS00278	Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.	ETXB_STAAU	179-202	2	B:152-175 D:152-175

(no "Exon" information available for 1SBB)

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:238
 aligned with TCB1_MOUSE | P01852 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:238
                                                                                                                                            1                                                                                                                             
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118        
           TCB1_MOUSE     - ----------------------------------------------------------------------------------------------------------------EDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD 126
               SCOP domains d1sbba1 A:3-117 T-cell antigen receptor                                                                          d1sbba2 A:118-246 T-cell antigen receptor                                                                                     SCOP domains
               CATH domains 1sbbA01 A:3-117 Immunoglobulins                                                                                  1sbbA02 A:118-246 Immunoglobulins                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee...............eee.......eeee....hhh.eeeeeeee........eee...eeeeee..hhh....eeeeee..hhh........eeeeeeee....eeeeeee..eee...eee....eeee..eeeeeeee...hhhh.....eeeeeeee...................eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sbb A   3 AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD 246
                                    12        22        32        42        52        62||      73        83        93       105       115|||    124       134       144       154       164       174       187|      198       208       218       228       238        
                                                                                       63|                                  102|        116||                                                              182|||                                                         
                                                                                        65                                   105         250|                                                               186||                                                         
                                                                                                                                          117                                                                187|                                                         
                                                                                                                                                                                                              189

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with ETXB_STAAU | P01552 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:239
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
           ETXB_STAAU    28 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 266
               SCOP domains d1sbbb1 B:1-121 Staphylococcal enterotoxin B, SEB                                                                        d1sbbb2 B:122-239 Staphylococcal enterotoxin B, SEB                                                                    SCOP domains
               CATH domains -1sbbB02 B:2-31,B:128-231      1sbbB01 B:32-121  [code=2.40.50.110, no name defined]                                     ------1sbbB02 B:2-31,B:128-231  [code=3.10.20.120, no name defined]                                           -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh...hhh....hhhhhhhh....eeeeee.........eeee...........eeeee...hhhhhhh....eeeee........................eeeee..eee.........eeeeeeeee..eeeeeeeeee...eeehhhhhhhhhhhhhhhh.........eeeeeeeee....eeeee..........hhhhhhhh....eee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------STAPH_STRE---------------------------STAPH_STREP_TOXIN_2     ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sbb B   1 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:238
 aligned with TCB1_MOUSE | P01852 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:238
                                                                                                                                            1                                                                                                                             
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118        
           TCB1_MOUSE     - ----------------------------------------------------------------------------------------------------------------EDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD 126
               SCOP domains d1sbbc1 C:3-117 T-cell antigen receptor                                                                          d1sbbc2 C:118-246 T-cell antigen receptor                                                                                     SCOP domains
               CATH domains 1sbbC01 C:3-117 Immunoglobulins                                                                                  1sbbC02 C:118-246 Immunoglobulins                                                                                             CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------C1-set-1sbbC01 C:131-224                                                                  ---------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------C1-set-1sbbC02 C:131-224                                                                  ---------------------- Pfam domains (2)
     Sec.struct. author (1) .eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee...............eee.......eeee....hhh.eeeeeeee..............eeeeee..hhh....eeeeee..hhh........eeeeeeee....------hhheee...eee....eeee..eeeeeeee...hhhhh....eeeeeeee...................eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sbb C   3 AVTQSPRNKVAVTGGKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQEQFSLILELATPSQTSVYFCASGGGRGSYAEQFFGPGTRLTVLEDLRQVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRAD 246
                                    12        22        32        42        52        62||      73        83        93       105       115|||    124       134       144       154       164       174       187|      198       208       218       228       238        
                                                                                       63|                                  102|        116||                                                              182|||                                                         
                                                                                        65                                   105         250|                                                               186||                                                         
                                                                                                                                          117                                                                187|                                                         
                                                                                                                                                                                                              189

Chain D from PDB  Type:PROTEIN  Length:235
 aligned with ETXB_STAAU | P01552 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:239
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
           ETXB_STAAU    28 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 266
               SCOP domains d1sbbd1 D:1-121 Staphylococcal enterotoxin B, SEB                                                                        d1sbbd2 D:122-239 Staphylococcal enterotoxin B, SEB                                                                    SCOP domains
               CATH domains -1sbbD02 D:2-31,D:128-231      1sbbD01 D:32-121  [code=2.40.50.110, no name defined]                                     ------1sbbD02 D:2-31,D:128-231  [code=3.10.20.120, no name defined]                                           -------- CATH domains
           Pfam domains (1) ----------------------Stap_Strp_toxin-1sbbD03 D:23-121                                                                   --------Stap_Strp_tox_C-1sbbD01 D:130-235                                                                         ---- Pfam domains (1)
           Pfam domains (2) ----------------------Stap_Strp_toxin-1sbbD04 D:23-121                                                                   --------Stap_Strp_tox_C-1sbbD02 D:130-235                                                                         ---- Pfam domains (2)
         Sec.struct. author .......hhh...hhh....hhhhhhhh....eee............eeeee..........eeeee...hhhhhhh....eeeee.............----.......eeeee..eee.........eeeeeeeee.....eeeeeee...eeehhhhhhhhhhhhhhhh.........eeeeeeeee....eeeee..........hhhhhhhh....eee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------STAPH_STRE---------------------------STAPH_STREP_TOXIN_2     ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sbb D   1 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKT----SHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 239
                                    10        20        30        40        50        60        70        80        90        |-   |   110       120       130       140       150       160       170       180       190       200       210       220       230         
                                                                                                                             99  104

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/Biological 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)

House mouse (Mus musculus) (7)

1a	1sbbB02	B:2-31,B:128-231
1b	1sbbD02	D:2-31,D:128-231

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)

House mouse (Mus musculus) (7)

2a	1sbbB01	B:32-121
2b	1sbbD01	D:32-121

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

3a	1sbbA01	A:3-117
3b	1sbbC01	C:3-117
3c	1sbbA02	A:118-246
3d	1sbbC02	C:118-246

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Staphylococcus aureus (41)

1a	Stap_Strp_tox_C-1sbbD01	D:130-235
1b	Stap_Strp_tox_C-1sbbD02	D:130-235

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

2a	C1-set-1sbbC01	C:131-224
2b	C1-set-1sbbC02	C:131-224

Clan: no clan defined [family: Stap_Strp_toxin] (39)

Family: Stap_Strp_toxin (39)

Staphylococcus aureus (33)

3a	Stap_Strp_toxin-1sbbD03	D:23-121
3b	Stap_Strp_toxin-1sbbD04	D:23-121

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (TCB1_MOUSE | P01852)

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.

Chain B,D (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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(no "Sites" information available for 1sbb)

	Cis Peptide Bonds
		Phe A:153 - Pro A:154	[ RasMol ]
		Phe C:153 - Pro C:154	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]

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	1sbb
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(no "Related Entries Specified in the PDB File" available for 1SBB)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

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