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(-) Description

Title :  STRUCTURE OF A HIGH-AFFINITY MUTANT OF THE 2C TCR IN COMPLEX WITH LD/QL9
 
Authors :  K. C. Garcia, L. A. Colf
Date :  11 Jan 07  (Deposition) - 24 Apr 07  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,P,Q
Biol. Unit 1:  A,D,E,Q  (1x)
Biol. Unit 2:  B,C,F,P  (1x)
Keywords :  Tcr, Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Colf, A. J. Bankovich, N. A. Hanick, N. A. Bowerman, L. L. Jones, D. M. Kranz, K. C. Garcia
How A Single T Cell Receptor Recognizes Both Self And Foreign Mhc.
Cell(Cambridge, Mass. ) V. 129 135 2007
PubMed-ID: 17418792  |  Reference-DOI: 10.1016/J.CELL.2007.01.048

(-) Compounds

Molecule 1 - CYTOTOXIC TCELL RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET22B
    Fragment: UNP RESIDUES 21-132
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: V ALPHA, T CELL RECEPTOR ALPHA CHAIN
 
Molecule 2 - BETA-CHAIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET22B
    Fragment: UNP RESIDUES 30-144
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: V BETA, T CELL RECEPTOR BETA CHAIN
 
Molecule 3 - H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, L-D ALPHA CHAIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET28A
    Fragment: ALPHA 1,2 DOMAINS (UNP RESIDUES 25-205)
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MAJOR HISTOCOMPATIBILITY COMPLEX PROTEIN
 
Molecule 4 - PEPTIDE (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)
    Chains: P, Q
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFPQ
Biological Unit 1 (1x): A  DE  Q
Biological Unit 2 (1x):  BC  FP 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2E7L)

(-) Sites  (0, 0)

(no "Site" information available for 2E7L)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:22 -A:90
2B:22 -B:90
3C:23 -C:92
4D:23 -D:92
5E:101 -E:164
6F:101 -F:164

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser C:7 -Pro C:8
2Ser D:7 -Pro D:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E7L)

(-) Exons   (0, 0)

(no "Exon" information available for 2E7L)

(-) 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:112
 aligned with A2NTU7_MOUSE | A2NTU7 from UniProtKB/TrEMBL  Length:268

    Alignment length:112
                                    30        40        50        60        70        80        90       100       110       120       130  
         A2NTU7_MOUSE    21 QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFCAVSGFASALTFGSGTKVIVLPY 132
               SCOP domains d2e7la_ A: automated matches                                                                                     SCOP domains
               CATH domains 2e7lA00 A:1-117 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee....eee..ee.......eeeeee......eeeeee.....eee....eeeeee....eeeeee...hhhhh.eeeeeee.....eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l A   1 QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSHQGRYLTFGSGTKVIVLPY 117
                                    10        20        30        40        50        60        70        80        90  ||   105       115  
                                                                                                                       93|                  
                                                                                                                        99                  


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with A2NTU7_MOUSE | A2NTU7 from UniProtKB/TrEMBL  Length:268

    Alignment length:110
                                    31        41        51        61        71        81        91       101       111       121       131
         A2NTU7_MOUSE    22 SVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFCAVSGFASALTFGSGTKVIVLP 131
               SCOP domains d2e7lb_ B: automated matches                                                                                   SCOP domains
               CATH domains 2e7lB00 B:2-116 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeee....eee..ee.......eeeeee......eeeeee.....eee....eeeeee....eeeeee...hhhhheeeeeeeee...eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l B   2 SVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSHQGRYLTFGSGTKVIVLP 116
                                    11        21        31        41        51        61        71        81        91 ||    106       116
                                                                                                                      93|                 
                                                                                                                       99                 


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with A2NTY6_MOUSE | A2NTY6 from UniProtKB/TrEMBL  Length:144

    Alignment length:117
                                                                                                                                            144  
                                    39        49        59        69        79        89        99       109       119       129       139    |  
         A2NTY6_MOUSE    30 EAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGELGGFNQDTQYFGPGTRLLVL--   -
               SCOP domains d2e7lc_ C: automated matches                                                                                          SCOP domains
               CATH domains 2e7lC00 C:1-119 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee......eeee.......eeee...hhhhheeeeeeee...-----..ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l C   1 EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIYYSYGAGSTEKGDIPDGYKASRPSQENFSLTLESATPSQTSVYFCASGGGG-----TLYFGAGTRLSVLSS 119
                                    10        20        30        40        50        60  ||    71        81        91      |  -  |    112       
                                                                                         63|                               98   105              
                                                                                          65                                                     


Chain D from PDB  Type:PROTEIN  Length:112
 aligned with A2NTY6_MOUSE | A2NTY6 from UniProtKB/TrEMBL  Length:144

    Alignment length:117
                                                                                                                                            144  
                                    39        49        59        69        79        89        99       109       119       129       139    |  
         A2NTY6_MOUSE    30 EAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGELGGFNQDTQYFGPGTRLLVL--   -
               SCOP domains d2e7ld_ D: automated matches                                                                                          SCOP domains
               CATH domains 2e7lD00 D:1-119 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee......eeee.......eeee...hhhhheeeeeeee...-----..ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l D   1 EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIYYSYGAGSTEKGDIPDGYKASRPSQENFSLTLESATPSQTSVYFCASGGGG-----TLYFGAGTRLSVLSS 119
                                    10        20        30        40        50        60  ||    71        81        91      |  -  |    112       
                                                                                         63|                               98   105              
                                                                                          65                                                     


Chain E from PDB  Type:PROTEIN  Length:175
 aligned with HA1L_MOUSE | P01897 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:175
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     
           HA1L_MOUSE    25 GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2e7lE00 E:1-175 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l E   1 GPHSMRYFETAVSRRGLGEPRYISVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYWERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain F from PDB  Type:PROTEIN  Length:175
 aligned with HA1L_MOUSE | P01897 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:175
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     
           HA1L_MOUSE    25 GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2e7lF00 F:1-175 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7l F   1 GPHSMRYFETAVSRRGLGEPRYISVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYWERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2e7l P   1 QLSPFPFDL   9


Chain Q from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2e7l Q   1 QLSPFPFDL   9
   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  (1, 4)

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

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E7L)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A2NTU7_MOUSE | A2NTU7)

Chain C,D   (A2NTY6_MOUSE | A2NTY6)

Chain E,F   (HA1L_MOUSE | P01897)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    GO:0071556    integral component of lumenal side of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
    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:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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.

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  2e7l
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  A2NTU7_MOUSE | A2NTU7
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  HA1L_MOUSE | P01897
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NTY6_MOUSE | A2NTY6: 3mc0 3owe
        HA1L_MOUSE | P01897: 1ld9 1ldp 2oi9 3e2h 3e3q 3ery 3tf7 3tfk 3tjh 3tpu 3uo1 3uyr 3v4u 3v52 3vj6 4ms8 4mvb 4mxq 4n0c 4n5e 4nhu
UniProtKB/TrEMBL
        A2NTY6_MOUSE | A2NTY6: 2icw 2oi9 2pxy 2z31 2z35 3e2h 4y16 4y2d 4y4f 4y4h 4y4k 4zak

(-) Related Entries Specified in the PDB File

2oi9