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(-) Description

Title :  CRYSTAL STRUCTURE OF CLONE42 TCR
 
Authors :  S. Gras, M. Bhati, J. Rossjohn
Date :  23 Jul 12  (Deposition) - 08 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tcr, T Cell, Cd1B, Gmm, Lipid Recognition, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Van Rhijn, A. Kasmar, A. De Jong, S. Gras, M. Bhati, M. E. Doorenspleet, N. De Vries, D. I. Godfrey, J. D. Altman, W. De Jager, J. Rossjohn, D. B. Moody
A Conserved Human T Cell Population Targets Mycobacterial Antigens Presented By Cd1B.
Nat. Immunol. V. 14 706 2013
PubMed-ID: 23727893  |  Reference-DOI: 10.1038/NI.2630

(-) Compounds

Molecule 1 - ALPHA CHAIN CLONE 42 TCR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - BETA CHAIN CLONE 42 TCR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4G8F)

(-) Sites  (0, 0)

(no "Site" information available for 4G8F)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:104
2A:150 -A:200
3A:175 -B:183
4B:23 -B:104
5B:157 -B:222

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ala A:46 -Gly A:47
2Asp A:59 -Gly A:60
3Ser A:196 -Asp A:197
4Thr B:7 -Pro B:8
5Gly B:47 -Met B:48
6Asp B:74 -Gly B:75
7Leu B:110 -Ala B:111
8Gly B:112 -Asp B:113
9Tyr B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G8F)

(-) Exons   (0, 0)

(no "Exon" information available for 4G8F)

(-) 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:184
                                                                                                                                                                                                                        
               SCOP domains d4g8fa1 A:3-128 automated matches                                                                          d4g8fa2 A:129-205 automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeeeee........eeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeeee........eeeeeee......eeeeee...............eee...eeee......eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8f A   3 NIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAVRNGFKTIFGAGTRLFVKANIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFN 205
                               ||   13        23        39        49        59||   || 81   |||  88        98       108|      121       131       141       151       161       171       181       191       201    
                               6|                      32|                   60|  70|    84A||                     108|                                                                                             
                                8                       39                    66   78     84B|                      112                                                                                             
                                                                                           84C                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4g8fb1 B:1-127 automated matches                                                                                 d4g8fb2 B:128-256 automated matches                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee........ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8f B   1 NAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEVPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSPRLAGDEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 256
                                    10        20        30||      47        57   ||   71||      83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
                                                         31|                    61|    72|     81|                                                                                                                                                                             
                                                          39                     66     74      83
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G8F)

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4g8f)
 
  Sites
(no "Sites" information available for 4g8f)
 
  Cis Peptide Bonds
    Ala A:46 - Gly A:47   [ RasMol ]  
    Asp A:59 - Gly A:60   [ RasMol ]  
    Asp B:74 - Gly B:75   [ RasMol ]  
    Gly B:112 - Asp B:113   [ RasMol ]  
    Gly B:47 - Met B:48   [ RasMol ]  
    Leu B:110 - Ala B:111   [ RasMol ]  
    Ser A:196 - Asp A:197   [ RasMol ]  
    Thr B:7 - Pro B:8   [ RasMol ]  
    Tyr B:163 - Pro B:164   [ RasMol ]  
 

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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 3qeu 3qib 3qjf 3qux 3scm 3sda 3sdc 3sdd 3sdx 3sjv 3skn 3t0e 3tn0 3tvm 4apq 4c56 4g8e 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
        TRBC1_HUMAN | P01850: 1ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 2iam 2ian 2nts 2nw2 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3d3v 3dx9 3dxa 3ffc 3he6 3hg1 3kpr 3kps 3o4l 3tn0 4g8e 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcc 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozf 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh

(-) Related Entries Specified in the PDB File

4g8e 4g8g 4g8i 4g9d 4g9f