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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TCR DMF5
 
Authors :  O. Y. Borbulevych, S. M. Santhanagopolan, B. M. Baker
Date :  20 Jan 11  (Deposition) - 06 Jul 11  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  D,E  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Mart-1 Peptide, Nonapeptide, Mhc Class I, Hla-A2, Tcr Dmf5, Tcr Dmf4, Cross-Reactivity, Cancer, Melanoma, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Y. Borbulevych, S. M. Santhanagopolan, M. Hossain, B. M. Baker
Tcrs Used In Cancer Gene Therapy Cross-React With Mart-1/Melan-A Tumor Antigens Via Distinct Mechanisms.
J. Immunol. V. 187 2453 2011
PubMed-ID: 21795600  |  Reference-DOI: 10.4049/JIMMUNOL.1101268

(-) Compounds

Molecule 1 - DMF5 ALPHA CHAIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHN1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DMF5 BETA CHAIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHN1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x):   DE
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2LI1Ligand/IonLITHIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LI-1Ligand/IonLITHIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LI-1Ligand/IonLITHIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1 , ASP D:138 , HOH D:207 , HOH D:260 , HOH D:286 , HOH D:497 , HOH D:498BINDING SITE FOR RESIDUE LI D 202
2AC2SOFTWAREGLN E:181 , HOH E:251 , HOH E:470BINDING SITE FOR RESIDUE GOL E 2
3AC3SOFTWAREMET B:30 , HOH B:354 , HIS E:32 , LEU E:98 , PHE E:105 , HOH E:252 , HOH E:413BINDING SITE FOR RESIDUE GOL B 246

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:22 -A:88
2A:157 -B:172
3B:26 -B:94
4B:146 -B:211
5D:22 -D:88
6D:132 -D:182
7D:157 -E:172
8E:26 -E:94
9E:146 -E:211

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly D:8 -Pro D:9
2Ala E:10 -Pro E:11
3Tyr E:152 -Pro E:153
4Gly A:8 -Pro A:9
5Ala B:10 -Pro B:11
6Tyr B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QEU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QEU)

(-) Exons   (0, 0)

(no "Exon" information available for 3QEU)

(-) 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:195
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:201
                                                                                                                                        1                                                                                            
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92 
            TCA_HUMAN     - ------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE  93
               SCOP domains d3qeua1 A:1-110 automated matches                                                                             d3qeua2 A:111-201 automated matches                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee....eeeeeee......eeeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeeee.....eee...eeeeee........eeeeeee.......eeeee................ee...eeeee....eeeeeeeee------..................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qeu A   1 KEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW------ACANAFNNSIIPEDTFFPSPE 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |     -|      190       200 
                                                                                                                                                                                                       174    181                    


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d3qeub1 B:4-117 automated matches                                                                                 d3qeub2 B:118-241 automated matches                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eee.........eee...hhhhheeeeeeee.......ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh.....eeeeeee..................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qeu B   4 IAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGEVPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSLSFGTEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW 241
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        


Chain D from PDB  Type:PROTEIN  Length:202
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:202
                                                                                                                                         1                                                                                            
                                     -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91  
            TCA_HUMAN     - -------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE  93
               SCOP domains d3qeud1 D:0-110 automated matches                                                                              d3qeud2 D:111-201 automated matches                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeee....eeeeeee....eeeeeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeeeee....eee...eeeeee........eeeeee.......eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qeu D   0 AKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE 201
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  


Chain E from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d3qeue1 E:3-117 automated matches                                                                                  d3qeue2 E:118-245 automated matches                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeeee..eeee......eee.........eee...hhhhheeeeeeee.......ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qeu E   3 MIAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGEVPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSLSFGTEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
   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  (3, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QEU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QEU)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (TCA_HUMAN | P01848)
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: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.

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  3qeu
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 Related Entries

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

UniProtKB/Swiss-Prot
        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 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 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb

(-) Related Entries Specified in the PDB File

3qdg 3qdj 3qdm 3qeq