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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S54N VARIANT OF MURINE T CELL RECEPTOR VBETA 8.2 DOMAIN
 
Authors :  S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M R. A. Mariuzza, E. J. Sundberg
Date :  16 Aug 05  (Deposition) - 21 Mar 06  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  T Cell Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M. Kranz, R. A. Mariuzza, E. J. Sundberg
Structural Basis Of Affinity Maturation And Intramolecular Cooperativity In A Protein-Protein Interaction.
Structure V. 13 1775 2005
PubMed-ID: 16338399  |  Reference-DOI: 10.1016/J.STR.2005.08.015

(-) Compounds

Molecule 1 - T-CELL RECEPTOR BETA CHAIN V
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:28 , ARG A:44 , ASP A:59 , GLY A:96 , THR A:99 , HOH A:202 , HOH A:241 , HOH A:246 , HOH A:295 , HOH A:306 , HOH A:311BINDING SITE FOR RESIDUE MLA A 200

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:92

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2APB)

(-) 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:110
 aligned with A2NAI0_RAT | A2NAI0 from UniProtKB/TrEMBL  Length:95

    Alignment length:110
                                                                                                                        95                
                                    11        21        31        41        51        61        71        81        91   |     -         -
           A2NAI0_RAT     2 EAAVTQSPRNKVTVTGKNVTFNCHQTDNHNYMYWYRQDMGHGLRLIHYSYGSGSFENGDIPEGYKVSRPNQENFFLTLESASPSQTSVYFCASS----------------   -
               SCOP domains d2apba_ A: automated matches                                                                                   SCOP domains
               CATH domains 2apbA00 A:1-117 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee.......eeeeee..eeeeee...hhhhheeeeeeee.....ee...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2apb A   1 EAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYKASRPSQEQFSLILESATPSQTSVYFCASGGGGTLYFGAGTRLSVL 117
                                    10        20        30        40        50        60  ||    71        81        91       101|      117
                                                                                         63|                                 101|         
                                                                                          65                                  108         


Chain A from PDB  Type:PROTEIN  Length:110
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:114
                                    18        28        38        48        58        68        78        88        98       108       118    
           TVB5_MOUSE     9 EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL 122
               SCOP domains d2apba_ A: automated matches                                                                                       SCOP domains
               CATH domains 2apbA00 A:1-117 Immunoglobulins                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee.......eeeeee..eeeeee...hhhhheeeeeeee...----..ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2apb A   1 EAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYKASRPSQEQFSLILESATPSQTSVYFCASGGGG----TLYFGAGTRLSVL 117
                                    10        20        30        40        50        60  ||    71        81        91      |  - | ||  113    
                                                                                         63|                               98   99 ||         
                                                                                          65                                     101|         
                                                                                                                                  108
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2APB)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2APB)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TVB5_MOUSE | P04213: 1d9k 1lp9 1u3h 2apf 2apt 2apv 2apw 2apx 2aq1 2aq2 2aq3 2icw 2j8u 2uwe 4nhu
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        A2NAI0_RAT | A2NAI0: 2apf 2apt 2apv 2apw 2apx

(-) Related Entries Specified in the PDB File

1tcr MURINE T-CELL ANTIGEN RECEPTOR 2C CLONE
2apf THE G17E/A52V/S54N/K66E/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apt THE G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apv THE G17E/A52V/S54N/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apw THE G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apx THE G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2aq1 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ E80V/L81S/T87S/G96V) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq2 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq3 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT