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(-) Description

Title :  CRYSTAL STRUCTURE OF 9C2 TCR BOUND TO CD1D
 
Authors :  A. P. Uldrich, J. Le Nours, D. G. Pellicci, S. Gras, J. Rossjohn, D. I. Go
Date :  01 Jul 13  (Deposition) - 02 Oct 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym./Biol. Unit :  A,B,D,G
Keywords :  Nkt Cells, Gammadelta Tcr, Cd1D, Lipid Recognition, Pbs-44, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Uldrich, J. Le Nours, D. G. Pellicci, N. A. Gherardin, K. G. Mcpherson, R. T. Lim, O. Patel, T. Beddoe, S. Gras, J. Rossjohn, D. I. Godfrey
Cd1D-Lipid Antigen Recognition By The Gamma Delta Tcr.
Nat. Immunol. V. 14 1137 2013
PubMed-ID: 24076636  |  Reference-DOI: 10.1038/NI.2713

(-) Compounds

Molecule 1 - ANTIGEN-PRESENTING GLYCOPROTEIN CD1D
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBACP10PH
    Expression System Taxid: 7111
    Expression System Vector Type: PLASMID
    Gene: CD1D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: R3G1
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBACP10PH
    Expression System Taxid: 7111
    Expression System Vector Type: PLASMID
    Gene: B2M, CDABP0092, HDCMA22P
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - 9C2 TCR DELTA CHAIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - 9C2 TCR GAMMA CHAIN
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3JLS1Ligand/Ion(15Z)-N-[(2S,3S,4R)-1-(ALPHA-D-GALACTOPYRANOSYLOXY)-3,4-DIHYDROXYOCTADECAN-2-YL]TETRACOS-15-ENAMIDE
4MG1Ligand/IonMAGNESIUM ION
5NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG A:305BINDING SITE FOR RESIDUE BMA A 306
2AC2SOFTWARELEU A:13 , GLN A:14 , PHE A:70 , VAL A:72 , TYR A:73 , SER A:76 , PHE A:77 , ARG A:79 , ASP A:80 , PHE A:84 , PHE A:114 , PHE A:118 , ASP A:151 , TRP A:153 , THR A:154 , LEU A:161 , PHE A:169 , HOH A:401 , HOH A:412 , ARG G:103 , TYR G:111BINDING SITE FOR RESIDUE JLS A 308
3AC3SOFTWAREARG G:103BINDING SITE FOR RESIDUE CL G 301
4AC4SOFTWAREALA A:19 , ASN A:20 , TRP A:23BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 20 RESIDUES 302 TO 303
5AC5SOFTWARETRP A:23 , THR A:24 , ARG A:25 , ASN A:42 , BMA A:306BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 42 RESIDUES 304 TO 305
6AC6SOFTWAREGLY A:128 , GLN A:159 , ASN A:163BINDING SITE FOR MONO-SACCHARIDE NAG A 301 BOUND TO ASN A 163
7AC7SOFTWAREASN D:134 , ILE G:138 , LEU G:140BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 134 RESIDUES 401 TO 403

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1D:26 -D:94
2G:26 -G:98

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1His B:31 -Pro B:32
2Asp D:98 -Pro D:99
3Tyr D:146 -Pro D:147
4Arg G:103 -Gly G:104
5Phe G:162 -Pro G:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LHU)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains d4lhua1 A:6-183 CD1, alpha-1 and alpha-2 domains                                                                                                                                  d4lhua2 A:184-277 automated matches                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....eeeeeeeee..eeeeee......eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.....eeeeeeeee..eeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.........eeeeeeeeee.....eeeee.........ee...ee.....eeeeeeeee.hhhhh..eeeee........ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lhu A   6 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYW 277
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275  


Chain B from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains d4lhub_ B: beta2-microglobulin                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee......ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4lhu B   0 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99


Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains d4lhud1 D:5-120 automated matches                                                                                   d4lhud2 D:121-206 automated matches                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeee....eee..eee.......eeeeee.....eeeeee........ee..eeeeee....eeeeee...hhhhh.eeeeeee.........eee...eeeeee..............ee..ee.ee...........ee.......................ee...........ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lhu D   5 QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDPGGLNTDKLIFGKGTRVTVEPRSQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLGKYEDSNSVTCSVQHDNKTVHSTDFE 206
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  


Chain G from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains d4lhug1 G:10-125 automated matches                                                                                  d4lhug2 G:126-236 automated matches                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeee.........eeeeeee......eeeeeee....eeee........eeee.......eeee...hhhhheeeeeeeee.........eeee...eeeeee..........eeee...hhhhhhhh.eeeeeeeeeee.....ee.............ee...eee..eeeeeeeeeee.hhh...eeeeee.........eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lhu G  10 GTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRGNPKTHYYKKLFGSGTTLVVTDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQEGNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIKTDV 236
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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  (4, 7)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (79, 88)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg G:103 - Gly G:104   [ RasMol ]  
    Asp D:98 - Pro D:99   [ RasMol ]  
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    Phe G:162 - Pro G:163   [ RasMol ]  
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  4lhu
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  B2MG_HUMAN | P61769
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  CD1D_HUMAN | P15813
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  Q6PJ56_HUMAN | Q6PJ56
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_HUMAN | P61769: 1a1m 1a1n 1a1o 1a6z 1a9b 1a9e 1agb 1agc 1agd 1age 1agf 1akj 1ao7 1b0g 1b0r 1bd2 1c16 1ce6 1cg9 1de4 1duy 1duz 1e27 1e28 1eey 1eez 1efx 1exu 1gzp 1gzq 1hhg 1hhh 1hhi 1hhj 1hhk 1hla 1hsa 1hsb 1i1f 1i1y 1i4f 1i7r 1i7t 1i7u 1im3 1im9 1jf1 1jgd 1jge 1jht 1jnj 1k5n 1kpr 1ktl 1lds 1lp9 1m05 1m6o 1mhe 1mi5 1n2r 1of2 1oga 1ogt 1onq 1p7q 1py4 1q94 1qew 1qlf 1qqd 1qr1 1qrn 1qse 1qsf 1qvo 1r3h 1s8d 1s9w 1s9x 1s9y 1sys 1syv 1t1w 1t1x 1t1y 1t1z 1t20 1t21 1t22 1tmc 1tvb 1tvh 1uqs 1ur7 1uxs 1uxw 1vgk 1w0v 1w0w 1w72 1x7q 1xh3 1xr8 1xr9 1xz0 1ydp 1ypz 1zhk 1zhl 1zs8 1zsd 1zt4 1zvs 2a83 2ak4 2av1 2av7 2axf 2axg 2bck 2bnq 2bnr 2bsr 2bss 2bst 2bvo 2bvp 2bvq 2c7u 2cii 2cik 2clr 2d31 2d4d 2d4f 2dyp 2e8d 2esv 2f53 2f54 2f74 2f8o 2fyy 2fz3 2git 2gj6 2gt9 2gtw 2gtz 2guo 2h26 2h6p 2hjk 2hjl 2hla 2hn7 2j8u 2jcc 2nw3 2nx5 2p5e 2p5w 2po6 2pye 2rfx 2uwe 2v2w 2v2x 2vb5 2vlj 2vlk 2vll 2vlr 2x4n 2x4o 2x4p 2x4q 2x4r 2x4s 2x4t 2x4u 2x70 2x89 2xks 2xku 2xpg 2ypk 2ypl 2yxf 2z9t 3am8 3b3i 3b6s 3bgm 3bh8 3bh9 3bhb 3bo8 3bp4 3bp7 3bvn 3bw9 3bwa 3bxn 3bze 3bzf 3c9n 3cdg 3cii 3ciq 3czf 3d18 3d25 3d2u 3d39 3d3v 3dbx 3dhj 3dhm 3dtx 3dx6 3dx7 3dx8 3dxa 3ekc 3ffc 3fqn 3fqr 3fqt 3fqu 3fqw 3fqx 3ft2 3ft3 3ft4 3giv 3gjf 3gsn 3gso 3gsq 3gsr 3gsu 3gsv 3gsw 3gsx 3h7b 3h9h 3h9s 3hae 3hcv 3hg1 3hla 3hpj 3huj 3i6g 3i6k 3i6l 3ib4 3ixa 3jts 3kla 3kpl 3kpm 3kpn 3kpo 3kpp 3kpq 3kpr 3kps 3kww 3kxf 3kyn 3kyo 3l3d 3l3g 3l3i 3l3j 3l3k 3lkn 3lko 3lkp 3lkq 3lkr 3lks 3ln4 3ln5 3low 3loz 3lv3 3m17 3m1b 3mgo 3mgt 3mr9 3mrb 3mrc 3mrd 3mre 3mrf 3mrg 3mrh 3mri 3mrj 3mrk 3mrl 3mrm 3mrn 3mro 3mrp 3mrq 3mrr 3mv7 3mv8 3mv9 3myj 3myz 3mzt 3na4 3nfn 3o3a 3o3b 3o3d 3o3e 3o4l 3ov6 3ox8 3oxr 3oxs 3pwj 3pwl 3pwn 3pwp 3qda 3qdg 3qdj 3qdm 3qeq 3qfd 3qfj 3qzw 3rew 3rl1 3rl2 3rwj 3s6c 3sdx 3sjv 3skm 3sko 3spv 3t8x 3tid 3tie 3tlr 3tm6 3to2 3tzv 3u0p 3upr 3utq 3uts 3utt 3v5d 3v5h 3v5k 3vcl 3vfm 3vfn 3vfo 3vfp 3vfr 3vfs 3vft 3vfu 3vfv 3vfw 3vh8 3vri 3vrj 3vwj 3vwk 3vxm 3vxn 3vxo 3vxp 3vxr 3vxs 3vxu 3w0w 3w39 3wl9 3wlb 3wuw 3x11 3x12 3x13 3x14 4e0k 4e0l 4e5x 4en3 4eup 4f7m 4f7p 4f7t 4ftv 4fxl 4g8g 4g8i 4g9d 4g9f 4gkn 4gks 4gup 4hkj 4hwz 4hx1 4i48 4i4w 4jfd 4jfe 4jff 4jfo 4jfp 4jfq 4jqv 4jqx 4jrx 4jry 4k71 4k7f 4kdt 4l29 4l3c 4l3e 4l4t 4l4v 4lcw 4lcy 4lnr 4m8v 4mj5 4mj6 4mji 4mnq 4n0f 4n0u 4n8v 4nnx 4nny 4no0 4no2 4no3 4no5 4nqc 4nqd 4nqe 4nqv 4nqx 4nt6 4o2c 4o2e 4o2f 4ono 4pj5 4pj7 4pj8 4pj9 4pja 4pjb 4pjc 4pjd 4pje 4pjf 4pjg 4pjh 4pji 4pjx 4pr5 4pra 4prb 4prd 4pre 4prh 4pri 4prn 4prp 4qok 4qrp 4qrq 4qrr 4qrs 4qrt 4qru 4r9h 4ra3 4rah 4rmq 4rmr 4rms 4rmt 4rmu 4rmv 4rmw 4u1h 4u1i 4u1j 4u1k 4u1l 4u1m 4u1n 4u1s 4u6x 4u6y 4uq2 4uq3 4wc8 4wdi 4wj5 4wo4 4wu5 4wu7 4wuu 4ww2 4wwk 4x0s 4x6c 4x6d 4x6e 4x6f 4xxc 4z76 4z77 4z78 4zez 5b38 5b39 5bjt 5brz 5bs0 5bxf 5c07 5c08 5c09 5c0a 5c0b 5c0c 5c0d 5c0e 5c0f 5c0g 5c0i 5c0j 5c9j 5cfh 5cka 5ckg 5cs7 5csb 5csg 5d2l 5d2n 5d5m 5d7i 5d7j 5d7l 5d9s 5ddh 5def 5deg 5e00 5e6i 5e9d 5enw 5eo0 5eo1 5eot 5eu3 5eu4 5eu5 5eu6 5euo 5f7d 5f9j 5fa3 5fa4 5fdw 5gr7 5gsb 5gsr 5gsv 5gsx 5hga 5hgb 5hgd 5hgh 5hhm 5hhn 5hho 5hhp 5hhq 5hyj 5ib1 5ib2 5ib3 5ib4 5ib5 5ieh 5iek 5im7 5inc 5ind 5iro 5isz 5iue 5j1a 5jhd 5jzi 5knm 5l2j 5l2k 5men 5meo 5mep 5meq 5mer 5n1y 5swq 5t6w 5t6x 5t6y 5t6z 5t70 5u16 5u17 5u1r 5u2v 5u6q 5u72 5v5l 5v5m 5vgd 5vge 5xos 5xot 5xov
        CD1D_HUMAN | P15813: 1zt4 2po6 3huj 3sdx 3tzv 3u0p 3vwj 3vwk 4en3 4mng 4mq7 4wo4 4ww2 4wwk
        TRGC1_HUMAN | P0CF51: 4lfh
UniProtKB/TrEMBL
        Q6PJ56_HUMAN | Q6PJ56: 4lfh 4mng 4mnh 4ndm

(-) Related Entries Specified in the PDB File

4lfh