2NTS - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SEK-HVB5.1

Authors :   S. Gunther, A. K. Varma, B. Moza, E. J. Sundberg

Date :   08 Nov 06 (Deposition) - 26 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,P

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

Reference :   S. Gunther, A. K. Varma, B. Moza, K. J. Kasper, A. W. Wyatt, P. Zhu, A. K. Rahman, Y. Li, R. A. Mariuzza, J. K. Mccormick, E. J. Sundberg
A Novel Loop Domain In Superantigens Extends Their T Cell Receptor Recognition Site
J. Mol. Biol. V. 371 210 2007
PubMed-ID: 17560605 | Reference-DOI: 10.1016/J.JMB.2007.05.038

Molecule 1 - TRBC1 PROTEIN
	Chains	:	P
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRBC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRBV5-4 PROTEIN

Molecule 2 - STAPHYLOCOCCAL ENTEROTOXIN K
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SEK
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	93062
	Strain	:	COL

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NTS)

(no "Site" information available for 2NTS)

Asymmetric/Biological Unit

No.	Residues
1	P:23	-	P:92
2	P:148	-	P:213

Asymmetric/Biological Unit

No.	Residues
1	Thr P:7	-	Pro P:8
2	Tyr P:154	-	Pro P:155

(no "SAP(SNP)/Variant" information available for 2NTS)

(no "PROSITE Motif" information available for 2NTS)

(no "Exon" information available for 2NTS)

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:217
 aligned with O54476_STAAU | O54476 from UniProtKB/TrEMBL  Length:242

    Alignment length:217
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       
         O54476_STAAU    24 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQCNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKLVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKE 240
               SCOP domains d2ntsa1 A:1-86 automated matches                                                      d2ntsa2 A:87-217 automated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Stap_Strp_toxin-2ntsA02 A:8-85                                                -------Stap_Strp_tox_C-2ntsA01 A:93-214                                                                                          --- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeee........eeeee....eeeee..hhhhhhh....eeeeee.eee.....eeee..eee...eeeeeee..eeeee..eeeee.....eeee.eeehhhhhhhhhhhhhhhhh.........hhhhh..........eeeeeeee....eeeee........hhhhhhhhhh...eee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nts A   1 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQSNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKA 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain P from PDB  Type:PROTEIN  Length:240
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:240
                                                                                                                                            1                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118       128
          TRBC1_HUMAN     - ----------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR 128
               SCOP domains d2ntsp1 P:3-118 automated matches                                                                                d2ntsp2 P:119-245 T-cell antigen receptor                                                                                       SCOP domains
               CATH domains 2ntsP01 P:3-118 Immunoglobulins                                                                                  2ntsP02 P:119-245 Immunoglobulins                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------C1-set-2ntsP01 P:132-225                                                                      -------------------- Pfam domains
         Sec.struct. author ..eee..eeeee....eeeeee......eeeeeeee...eeeeeeeee..eeeee......eeeee.....eeeee...hhhhheeeeeeee.........ee...eeeeee.hhhhh...eeeee.............eeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeee...........eeeeeeee..................eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nts P   3 GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFNETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLADRVNTEAFFGQGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR 245
                                    12        22        32        42        52        62|       73        83        93       103|      115       125       135       145       155       165       175       185       195       205       215       225       235       245
                                                                                      62|                                    103|                                                                                                                                           
                                                                                       64                                     106

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: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	2ntsP01	P:3-118
1b	2ntsP02	P:119-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ant-toxin_C (48)

Family: Stap_Strp_tox_C (48)

Staphylococcus aureus (41)

Stap_Strp_tox_C-2ntsA01

A:93-214

Clan: Ig (577)

Family: C1-set (338)

Homo sapiens (Human) (218)

C1-set-2ntsP01

P:132-225

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

Family: Stap_Strp_toxin (39)

Staphylococcus aureus (33)

Stap_Strp_toxin-2ntsA02

A:8-85

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (O54476_STAAU | O54476)

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.

Chain P (TRBC1_HUMAN | P01850)

biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
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/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2nts)

	Sites
(no "Sites" information available for 2nts)

	Cis Peptide Bonds
		Thr P:7 - Pro P:8	[ RasMol ]
		Tyr P:154 - Pro P:155	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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SCOP Domains (4, 4)

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