Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN E IN COMPLEX WITH A T CELL RECEPTOR
 
Authors :  K. E. J. Rodstrom, P. Regenthal, K. Lindkvist-Petersson
Date :  15 Oct 15  (Deposition) - 25 May 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Immune System, Superantigen, Staphylcococcal Enterotoxin, T Cell Receptor, Major Histocompatibility Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. J. Rodstrom, P. Regenthal, C. Bahl, A. Ford, D. Baker, K. Lindkvist-Petersson
Two Common Structural Motifs For Tcr Recognition By Staphylococcal Enterotoxins.
Sci. Rep. V. 6 25796 2016
PubMed-ID: 27180909  |  Reference-DOI: 10.1038/SREP25796

(-) Compounds

Molecule 1 - T CELL RECEPTOR ALPHA CHAIN
    Cell: T-LYMPHOCYTE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PGMT7
    Expression System Vector Type: PLASMID
    Fragment: IMMUNOGLOBULIN DOMAINS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: VARIABLE DOMAIN TRAV22 AND CONSTANT DOMAIN TRAC1
 
Molecule 2 - T CELL RECEPTOR BETA CHAIN
    Cell: T-LYMPHOCYTE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PGMT7
    Expression System Vector Type: PLASMID
    Fragment: IMMUNOGLOBULIN DOMAINS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: VARIABLE DOMAIN TRBV7-9 AND CONSTANT DOMAIN TRBC2
 
Molecule 3 - STAPHYLOCOCCAL ENTEROTOXIN E
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Expression System Variant: UL 635
    Fragment: OB DOMAIN AND BETA GRASP DOMAIN, RESIDUES 1-233
    Gene: ENTA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:187 , HIS C:225 , ASP C:227 , HOH C:2030BINDING SITE FOR RESIDUE ZN C 300

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:88
2A:135 -A:185
3A:160 -B:170
4B:24 -B:93
5B:144 -B:209
6C:96 -C:106

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:8 -Pro A:9
2Asn B:8 -Pro B:9
3Tyr B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FKA)

(-) Exons   (0, 0)

(no "Exon" information available for 5FKA)

(-) Sequences/Alignments

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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee......eeeeee...eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeee........ee...eeeeee........................................eee...eeeee....eeeeeeeeee.....hhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fka A   2 GIQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNGQLINLFYIPSGTKQNGRLSATTVATERYSLLYISSSQTTDSGVYFCAVDSAGTYKYIFGTGTRLKVLANIQNPDPAVYQLRDSKDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE 204
                                    11        21        31       |43        53        63        73        83        93|      105       115       125  ||   137       147       157       167       177       187       197       
                                                                39|                                                 93|                             128|                                                                         
                                                                 42                                                  96                              131                                                                         


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee......eeeeeee......eeeeeee..eeeee.......eeee......eeeee...hhhhheeeeeeee......ee...eeeeee.hhhhh..........hhhhhhhhh...............eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fka B   3 TGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLGGYEQYFGPGTRLTVTEDLKNVFPPEVAVFVPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 242
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhh..eeeeeeee........eeee...........eeeee..hhhhhhhhh..eeeeeeeee........eeeee..eee....eeeeeee..eeeee..eeee......eeee.eeehhhhhhhhhhhhhhhhh............eeeeeee.....eeeee.......hhhhhhhhhh...eee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fka C  10 KDLRKKSELQRNALSNLRQIYYYNEKAITENKESDDQFLENTLLFKGFFTGHPWYNDLLVDLGSKDATNKYKGKKVDLYGAYYGYQCAGNKTACMYGGVTLHDNNRLTEEKKVPINLWIDGKQTTVPIDKVKTSKKEVTVQELDLQARHYLHGKFGLYNSDSFGGKVQRGLIVFHSSEGSTVSYDLFDAQGQYPDTLLRIYRDNKTINSENLHIDLYLYTT 233
                                    19        29        39        49        59        69        79        89       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
                                                                                                                   98|                                                                                                                                   
                                                                                                                   102
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FKA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FKA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FKA)

(-) Gene Ontology  (9, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:8 - Pro B:9   [ RasMol ]  
    Ser A:8 - Pro A:9   [ RasMol ]  
    Tyr B:150 - Pro B:151   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5fka
    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
  A0A0B4J277_H | A0A0B4J277
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  A0A5A3_HUMAN | A0A5A3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  ETXE_STAAU | P12993
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TCA_HUMAN | P01848
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TRBC2_HUMAN | A0A5B9
    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

(-) Analysis Tools

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
  A0A0B4J277_H | A0A0B4J277
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  A0A5A3_HUMAN | A0A5A3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ETXE_STAAU | P12993
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TCA_HUMAN | P01848
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRBC2_HUMAN | A0A5B9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ETXE_STAAU | P12993: 1olv 1olw 1see 4udu
        TCA_HUMAN | P01848: 1ao7 1bd2 1fyt 1j8h 1kgc 1mi5 1oga 1qrn 1qsf 1ymm 1zgl 2ak4 2bnq 2bnr 2bnu 2cdf 2cdg 2esv 2eyr 2eys 2eyt 2f53 2f54 2gj6 2ial 2iam 2ian 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3dx9 3dxa 3ffc 3gsn 3he7 3hg1 3kpr 3kps 3kxf 3o4l 3o6f 3o8x 3o9w 3pwp 3qdg 3qdj 3qdm 3qeq 3qeu 3qib 3qjf 3qux 3scm 3sda 3sdc 3sdd 3sdx 3sjv 3skn 3t0e 3tn0 3tvm 4apq 4c56 4g8e 4g8f 4irs 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4prh 4pri 4prp 4udt 4udu 4ww1 4ww2 4wwk 4x6b 4x6c 4x6d 4y16 4y2d 4y4f 4y4h 4y4k 4zdh 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5hhm 5hho 5hyj 5ks9 5ksa 5ksb
        TRBC2_HUMAN | A0A5B9: 1ao7 1bd2 2eyr 2eys 2eyt 3kxf 3o6f 3o8x 3o9w 3qux 3t0e 3ta3 3tvm 4c56 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4udt 4udu 4ww1 4ww2 4wwk 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5hhm 5hho 5hyj 5ks9 5ksa 5ksb
UniProtKB/TrEMBL
        A0A0B4J277_H | A0A0B4J277: 4udt 4udu 5fk9
        A0A5A3_HUMAN | A0A5A3: 4udt 4udu 5fk9

(-) Related Entries Specified in the PDB File

5fk9 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN A IN COMPLEX WITH A T CELL RECEPTOR