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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN VALPHA7.2/VBETA13.3 MAIT TCR IN COMPLEX WITH BOVINE MR1
 
Authors :  J. Lopez-Sagaseta, E. J. Adams
Date :  17 Jun 13  (Deposition) - 16 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Immunoglobulin Domain, Mhc-Class I, Antigen Presentation, Antigen Recognition, Antigen, 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 - MUCCOSAL ASSOCIATED INVARIANT T CELL RECEPTOR ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - MUCCOSAL ASSOCIATED INVARIANT T CELL RECEPTOR BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - BETA-2-MICROGLOBULIN, MHC CLASS I-RELATED PROTEIN
    Chains: C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: MR1, BT.63045
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: FUSION PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1KFP1Mod. Amino AcidN~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:59 , LYS A:81 , HOH A:402BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREPRO A:7 , THR A:8 , GLU A:9BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREVAL B:166 , HIS B:167 , SER B:168BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWAREGLY B:163 , HIS B:207 , ARG B:209 , LYS C:297 , ARG C:299BINDING SITE FOR RESIDUE SO4 C 401
5AC5SOFTWARESER C:56 , LYS C:57BINDING SITE FOR RESIDUE SO4 C 402

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:88
2A:132 -A:182
3A:157 -B:171
4B:23 -B:91
5B:145 -B:210
6C:25 -C:79
7C:212 -C:275
8C:314 -C:370

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Thr B:7 -Pro B:8
2Asp B:97 -Pro B:98
3Gly B:101 -Glu B:102
4Tyr B:151 -Pro B:152
5His C:31 -Pro C:32
6Glu C:128 -Pro C:129
7Tyr C:320 -Pro C:321
8Asn C:331 -Gly C:332
9Gly C:376 -Val C:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L8S)

(-) Exons   (0, 0)

(no "Exon" information available for 4L8S)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains d4l8sa1 A:3-110 automated matches                                                                           d4l8sa2 A:111-200 automated matches                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeeee....eeeeeee......eeeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeeee.....eee...eeeeee........eeee.........eeeeee................eee...ee..........eeeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l8s A   3 NIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCASMDSNYQLIWGAGTKLIIKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP 200
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d4l8sb1 B:2-115 automated matches                                                                                 d4l8sb2 B:116-243 automated matches                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee.......eeee.....eeeee...hhhhheeeeeeee.........ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8s B   2 AGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSETDPNTGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  


Chain C from PDB  Type:PROTEIN  Length:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee...........eeeeeeee.....eeeeee..eee.eee...ee.....eeeeeee.........eeeeee.......eeee............eeeeeeeeee.........eeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee..eeeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l8s C   1 IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDGGGSGGRTHSLRYFRLGISEPGYGIPEFISAGYVDSHPITMYNSVSQLkEPRALWMEENLAPDHWERYTQLLRGWQQAFKVELKQLQHHYNHSGFHTYQRMIGCELLEDGSITGFLQYAYDGQDFLIFNKDTLSWMAMDNVADIIRRVWEANRHELQYQKNWLEEECIAWLKRFLEYGKDALQRTEPPKVRVNHKETITTLYCRAYGFYPPEISINWMKNGEEIFQDTDYGGILPSGDGTYQTWVSVELDPQNGDIYSCHVEHGGVHMVLQGFQE 386
                                    10        20        30        40        50        60        70        80        90      |102  ||   121       131       141       151     | 161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   ||  314       324       334       344       354       364       374       384  
                                                                                                                           97|  105|                                       157-KFP                                                                                                                                             305|                                                                             
                                                                                                                           100   115                                                                                                                                                                                            309
   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 4L8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L8S)

(-) Gene Ontology  (46, 54)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly B:101 - Glu B:102   [ RasMol ]  
    Gly C:376 - Val C:377   [ RasMol ]  
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    Thr B:7 - Pro B:8   [ RasMol ]  
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  4l8s
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_BOVIN | P01888: 1bmg 2xfx 3l9r 3pwv 4f7c 4f7e 4iiq 4l9l 4lcc
        HMR1_BOVIN | C1ITJ8: 4iiq 4l9l 4lcc
UniProtKB/TrEMBL
        Q6P4G7_HUMAN | Q6P4G7: 2nw2 4iiq 4l4v 4l9l 4lcc 4lcw 4nqc 4nqd 4nqe

(-) Related Entries Specified in the PDB File

4iiq SIMILAR COMPLEX WITH DIFFERENT MAIT TCR
4l9l