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(-) Description

Title :  1.B2.D9, A BISPECIFIC ALPHA/BETA TCR
 
Authors :  C. Mcbeth, J. C. Pizarro, R. K. Strong
Date :  06 Mar 07  (Deposition) - 05 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,C,E,G
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  E,G  (1x)
Keywords :  Tcr, Autoimmunity, Immunoglobulin Fold, Diabody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Mcbeth, A. Seamons, J. C. Pizarro, S. J. Fleishman, D. Baker, T. Kortemme, J. M. Goverman, R. K. Strong
A New Twist In Tcr Diversity Revealed By A Forbidden Alphabeta Tcr.
J. Mol. Biol. V. 375 1306 2008
PubMed-ID: 18155234  |  Reference-DOI: 10.1016/J.JMB.2007.11.020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BISPECIFIC ALPHA/BETA TCR
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21 DE3 (RIL)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VALPHA2.3/VBETA8.2
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: 1.B2.D9

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACEG
Biological Unit 1 (1x): AC  
Biological Unit 2 (1x):   EG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2P1Y)

(-) Sites  (0, 0)

(no "Site" information available for 2P1Y)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:92
2A:322 -A:390
3C:23 -C:92
4C:322 -C:390
5E:23 -E:92
6E:322 -E:390
7G:23 -G:92
8G:322 -G:390

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:306 -Pro A:307
3Ser C:7 -Pro C:8
4Ser C:306 -Pro C:307
5Ser E:7 -Pro E:8
6Ser E:306 -Pro E:307
7Leu E:411 -Pro E:412
8Ser G:7 -Pro G:8
9Ser G:306 -Pro G:307
10Leu G:411 -Pro G:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2P1Y)

(-) Sequences/Alignments

Asymmetric 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:231
 aligned with Q5R1B3_MOUSE | Q5R1B3 from UniProtKB/TrEMBL  Length:120

    Alignment length:231
                                                               2                                                                                                                                                                                                   
                                                              1|     3     9                      10      18        19 22                23    29   30                                                                                       120                   
                                     -         -         -    ||   - |     | -         -         - |      18        19  |      -         -|     |  - |      38        48        58        68        78        88        98       108       118 |       -         - 
         Q5R1B3_MOUSE     - ----------------------------------MD-----KILTASF-----------------------LLLGLHLAG---------VSGQ-----------------QEKRDQQ----QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAS-------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p1yA01 A:3-116 Immunoglobulins                                                                           ---------------2p1yA02 A:302-412 Immunoglobulins                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.......eeee...hhhhheeeeeeee...ee...eeeeee.hhhhhhhhhhhhhh..eee..eeeee....eeeeee.......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1y A   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDRLFFGHGTKLSVLGSADDAKKDAAKKDGQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSDKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAIDTNAYKVIFGKGTHLHVLP 412
                                    12        22        32        42        52        62||      73        83        93  ||   110       204       214||     310       320       330       340       350       361       371       381       391       401       411 
                                                                                       63|                             96|           118|         215|                                                      359|                                                   
                                                                                        65                             104            203          302                                                       361                                                   


Chain C from PDB  Type:PROTEIN  Length:231
 aligned with Q5R1B3_MOUSE | Q5R1B3 from UniProtKB/TrEMBL  Length:120

    Alignment length:231
                                                               2                                                                                                                                                                                                   
                                                              1|     3     9                      10      18        19 22                23    29   30                                                                                       120                   
                                     -         -         -    ||   - |     | -         -         - |      18        19  |      -         -|     |  - |      38        48        58        68        78        88        98       108       118 |       -         - 
         Q5R1B3_MOUSE     - ----------------------------------MD-----KILTASF-----------------------LLLGLHLAG---------VSGQ-----------------QEKRDQQ----QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAS-------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee...ee...eeeeee.hhhhhhhhhhhhhh..eee..eeeee....eeeeee.......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1y C   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDRLFFGHGTKLSVLGSADDAKKDAAKKDGQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSDKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAIDTNAYKVIFGKGTHLHVLP 412
                                    12        22        32        42        52        62||      73        83        93  ||   110     ||204       214||     310       320       330       340       350       361       371       381       391       401       411 
                                                                                       63|                             96|         116|           215|                                                      359|                                                   
                                                                                        65                             104          201            302                                                       361                                                   


Chain E from PDB  Type:PROTEIN  Length:217
 aligned with Q5R1B3_MOUSE | Q5R1B3 from UniProtKB/TrEMBL  Length:120

    Alignment length:217
                                  1  4 5     12                   13     20  21  25         26 29                                     30                                                                                       120                   
                                  |  4 |      |-         -        13      |  -|   |    -     |  |-         -         -         -       |32        42        52        62        72        82        92       102       112       | -         -       
         Q5R1B3_MOUSE     - ------MDKI-LTASFLLL--------------------GLHLAGVS---GQQEK----------RDQQ--------------------------------------QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAS-------------------   -
               SCOP domains d2p1ye1 E:3-116 automated matches                                                                         -d2p1ye2 E:302-412 automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eeeeee..eeeeee...hhhhheeeeeeee...ee...eeeeee..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1y E   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDRLFFGHGTKLSVLGQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSDKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAIDTNAYKVIFGKGTHLHVLP 412
                                    12        22        32        42        52        62||      73        83        93  ||   110      |304       314       324       334       344       354    || 365       375       385       395       405       
                                                                                       63|                             96|          117|                                                      359|                                                   
                                                                                        65                             104           302                                                       361                                                   


Chain G from PDB  Type:PROTEIN  Length:217
 aligned with Q5R1B3_MOUSE | Q5R1B3 from UniProtKB/TrEMBL  Length:120

    Alignment length:217
                                  1  4 5     12                   13     20  21  25         26 29                                     30                                                                                       120                   
                                  |  4 |      |-         -        13      |  -|   |    -     |  |-         -         -         -       |32        42        52        62        72        82        92       102       112       | -         -       
         Q5R1B3_MOUSE     - ------MDKI-LTASFLLL--------------------GLHLAGVS---GQQEK----------RDQQ--------------------------------------QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAS-------------------   -
               SCOP domains d2p1yg1 G:3-116 automated matches                                                                         -d2p1yg2 G:302-412 automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee...ee...eeeeee..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1y G   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDRLFFGHGTKLSVLGQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSDKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAAIDTNAYKVIFGKGTHLHVLP 412
                                    12        22        32        42        52        62||      73        83        93  ||   110     ||304       314       324       334       344       354    || 365       375       385       395       405       
                                                                                       63|                             96|         116||                                                      359|                                                   
                                                                                        65                             104          215|                                                       361                                                   
                                                                                                                                     302
   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  (2, 4)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P1Y)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P1Y)

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  Cis Peptide Bonds
    Leu E:411 - Pro E:412   [ RasMol ]  
    Leu G:411 - Pro G:412   [ RasMol ]  
    Ser A:306 - Pro A:307   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:306 - Pro C:307   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser E:306 - Pro E:307   [ RasMol ]  
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    Ser G:306 - Pro G:307   [ RasMol ]  
    Ser G:7 - Pro G:8   [ RasMol ]  
 
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 Related Entries

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UniProtKB/TrEMBL
        Q5R1B3_MOUSE | Q5R1B3: 1b88 1u3h

(-) Related Entries Specified in the PDB File

2p24