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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN MAIT TCR IN COMPLEX WITH A BACTERIAL ANTIGEN BOUND TO HUMANIZED BOVINE MR1
 
Authors :  J. Lopez-Sagaseta, E. J Adams
Date :  21 Jun 13  (Deposition) - 16 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.26
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Immunoglobulin Domain, Mhc-Class I-Like, Antigen Presentation, Antigen Recognition, B Vitamins Metabolites, Cell Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lopez-Sagaseta, C. L. Dulberger, A. Mcfedries, M. Cushman, A. Saghatelian, E. J. Adams
Mait Recognition Of A Stimulatory Bacterial Antigen Bound T Mr1.
J. Immunol. V. 191 5268 2013
PubMed-ID: 24108697  |  Reference-DOI: 10.4049/JIMMUNOL.1301958

(-) Compounds

Molecule 1 - BETA-2-MICROGLOBULIN, MHC CLASS I-RELATED PROTEIN
    ChainsC
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System PlasmidPACGP67A
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentP01888 RESIDUES 21-118, C1ITJ8 RESIDUES 19-295
    GeneMR1, BT.63045
    MutationYES
    Organism CommonBOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    Other DetailsFUSION PROTEIN
 
Molecule 2 - HUMAN MAIT TCR ALPHA CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainROSETTA (DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - HUMAN MAIT TCR BETA CHAIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainROSETTA (DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
11XL1Ligand/Ion1-DEOXY-1-[6-(HYDROXYMETHYL)-2,4-DIOXO-3,4-DIHYDROPTERIDIN-8(2H)-YL]-D-ARABINITOL
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:95 , GLU B:99 , TYR C:120 , PHE C:121 , ARG C:122 , SER C:137 , LYS C:156 , TYR C:175 , TRP C:182 , ARG C:207 , ILE C:209 , TYR C:265 , TRP C:269BINDING SITE FOR RESIDUE 1XL C 401
2AC2SOFTWARESER A:27 , ARG C:174 , TRP C:277 , ARG C:280BINDING SITE FOR RESIDUE SO4 C 402
3AC3SOFTWAREARG A:59 , GLN A:79 , LYS A:81BINDING SITE FOR RESIDUE SO4 A 301
4AC4SOFTWAREGLY B:164 , HIS B:208 , ARG B:210 , LYS C:296 , ARG C:298BINDING SITE FOR RESIDUE SO4 B 301
5AC5SOFTWAREVAL B:167 , HIS B:168 , SER B:169BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:88
2B:23 -B:91
3B:146 -B:211
4C:25 -C:79
5C:211 -C:274
6C:313 -C:369

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1His C:31 -Pro C:32
2Tyr C:319 -Pro C:320
3Asn C:330 -Gly C:331
4Gly C:375 -Val C:376
5Thr B:7 -Pro B:8
6Gly B:98 -Glu B:99
7Tyr B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LCC)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee....eeeeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhh.eeeeeee.....eeeeeeeeeeee........eeee.........eeeeee........eeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcc A   2 QNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDKDSDVYITDKKSNSAVAWSN 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |149      |170       
                                                                                                                                                                  138|      156|         
                                                                                                                                                                   147       168         

Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeeeee..eeee.......eeee....eeeeee...hhhhh.eeeeeee..........ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee.............eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcc B   2 AGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWKPVTQIVSAEAWGRA 244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  ||   236        
                                                                                                                                                                                                                                                        224|              
                                                                                                                                                                                                                                                         230              

Chain C from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeeeee.....eeeee....ee...ee.....eeeeeee........eeeee........eee....eeeeeeeeee.....eeeeeee..eeeeeee......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeee..eeeeeee....eeee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeeee.....eeeeee..ee....eeeeeeee.....eeeeeeee....eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcc C   1 IQRPPKIQVYSRHPPNYLNCYVYGFHPPQIEIDLLKIKSEQSDLSFSKDWSFYLLSHATPNSKDQYSCRVKHVTLEQPRIVKWDRTHSLRYFRLGISEIPEFISAGYVDSHPITMYNSVSQLKEPRALWMEENLAPDHWERYTQLLRGWQQMFKVELKQLQHHYNHSGFHTYQRMIGCELLEDGSITGFLQYAYDGQDFLIFNKDTLSWMAMDNVADIIRRVWEANQHELLYQKNWLEEECIAWLKRFLEYGKDALQRTEPPKVRVNHKTTLYCRAYGFYPPEISINWMKNGEEIFQDTDYGGILPSGDGTYQTWVSVELGDIYSCHVEHGGVHMVLQGFQ 384
                                    10   ||   25        35    ||  49        59       |71        81        91   ||  119       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       309       319       329       339       349       359|      373       383 
                                        14|                  40|                    67|                       95|          127|                                                                                                                                                                       302|                                               359|                    
                                         20                   45                     70                       114           132                                                                                                                                                                        309                                                364                    

   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  (0, 0)

(no "SCOP Domain" information available for 4LCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 61)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_BOVIN | P018881bmg 2xfx 3l9r 3pwv 4f7c 4f7e 4iiq 4l8s 4l9l
        HMR1_BOVIN | C1ITJ84iiq 4l8s 4l9l
        TRBC1_HUMAN | P018501ao7 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 4g8f 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozf 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh
UniProtKB/TrEMBL
        Q6P4G7_HUMAN | Q6P4G72nw2 4iiq 4l4v 4l8s 4l9l 4lcw 4nqc 4nqd 4nqe

(-) Related Entries Specified in the PDB File

4iiq SAME MAIT TCR COMPLEXED WITH BOVINE MR1 AND AN ANTIGEN OF NON-BACTERIAL ORIGIN
4l8s SIMILAR COMPLEX WITH BOVINE MR1 AND A MAIT TCR BEARING A BETA CHAIN OF DIFFERENT USAGE
4l9l SIMILAR COMPLEX WITH BOVINE MR1 AND A MAIT TCR BEARING A BETA CHAIN OF DIFFERENT USAGE