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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MCD1D/DB06-1/INKTCR TERNARY COMPLEX
 
Authors :  D. M. Zajonc, A. M. Birkholz
Date :  13 Apr 15  (Deposition) - 01 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Mhc-Fold, Ig-Fold, Glycolipid Antigen Presentation, T Cell Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Birkholz, E. Girardi, G. Wingender, A. Khurana, J. Wang, M. Zhao, S. Zahner, P. A. Illarionov, X. Wen, M. Li, W. Yuan, S. A. Porcelli, G. S. Besra, D. M. Zajonc, M. Kronenberg
A Novel Glycolipid Antigen For Nkt Cells That Preferentiall Induces Ifn-Gamma Production.
J Immunol. V. 195 924 2015
PubMed-ID: 26078271  |  Reference-DOI: 10.4049/JIMMUNOL.1500070

(-) Compounds

Molecule 1 - ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBACPHP10
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: TRANSFER VECTOR
    Gene: CD1D1, CD1.1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBACP10PH
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: TRANSFER VECTOR
    Gene: B2M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PROTEIN TRAV11,VA14JA18/VB8.2,HUMAN NKT TCR ALPHA CHAIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3), BL21DE3
    Expression System Taxid: 469008
    Gene: TRAV11, TRAV11D, TCR-ALPHA, B2M, HDCMA22P
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Synonym: PROTEIN TRAV11D,HUMAN NKT TCR BETA CHAIN
 
Molecule 4 - T CELL ANTIGEN RECEPTOR BETA CHAIN 8.2,T-CELL RECEPTOR BETA-2 CHAIN C REGION,PROTEIN TRBC2,T-CELL RECEPTOR BETA-2 CHAIN C REGION
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: TRBC2, TRBC2, TCRBC2
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
14LX1Ligand/IonN-[(2S,3S,4R)-1-(ALPHA-D-GALACTOPYRANOSYLOXY)-3,4-DIHYDROXYOCTADECAN-2-YL]HEXACOSANETHIOAMIDE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLN A:14 , SER A:28 , VAL A:30 , PHE A:70 , TYR A:73 , SER A:76 , ASP A:80 , LEU A:100 , TRP A:133 , ASP A:153 , GLY A:155 , THR A:156 , PHE A:171 , PRO C:29 , ASN C:31 , ASP C:94 , ARG C:95 , GLY C:96binding site for residue 4LX A 305
2AC2SOFTWAREALA A:19 , ASN A:20binding site for Mono-Saccharide NAG A 301 bound to ASN A 20
3AC3SOFTWARETRP A:23 , SER A:24 , ASN A:42binding site for Mono-Saccharide NAG A 302 bound to ASN A 42
4AC4SOFTWAREGLY A:130 , THR A:131 , GLN A:161 , ASN A:165binding site for Poly-Saccharide residues NAG A 303 through NAG A 304 bound to ASN A 165

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:168
2A:208 -A:263
3B:25 -B:80
4C:23 -C:90
5C:137 -C:187
6C:162 -D:168
7D:23 -D:91
8D:142 -D:207

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:89 -Pro A:90
2Tyr A:94 -Pro A:95
3Tyr A:214 -Pro A:215
4His B:31 -Pro B:32
5Ser C:7 -Pro C:8
6Thr C:28 -Pro C:29
7Ser D:7 -Pro D:8
8Tyr D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZAK)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeeeeee..eeeeee.......ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.....eeeeeeeee..eeeeeee..eeee....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeee........eeeeee........eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zak A   7 NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYW 279
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196||     212       222       232       242       252       262       272       
                                                                                                                                                                                                                        197|                                                                           
                                                                                                                                                                                                                         204                                                                           


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4zak B   2 QKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM  99
                                    11        21        31        41        51        61        71        81        91        


Chain C from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee.....eeeeeee...eeeeee..eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeeeee......eeeeee................ee...eeeeehhhheeeeeeeee......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zak C   2 TQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee......ee...eeeeee.........eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zak D   2 AAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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 4ZAK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 87)

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
        A2NTY6_MOUSE | A2NTY6: 3mc0 3owe
        B2MG_MOUSE | P01887: 1bii 1bqh 1bz9 1cd1 1ddh 1ffn 1ffo 1ffp 1fg2 1fo0 1fzj 1fzk 1fzm 1fzo 1g6r 1g7p 1g7q 1hoc 1inq 1jpf 1jpg 1juf 1k8d 1kbg 1kj2 1kj3 1kpu 1kpv 1l6q 1ld9 1ldp 1leg 1lek 1lk2 1mhc 1mwa 1n3n 1n59 1n5a 1nam 1nan 1nez 1osz 1p1z 1p4l 1pqz 1qo3 1rjy 1rjz 1rk0 1rk1 1s7q 1s7r 1s7s 1s7t 1s7u 1s7v 1s7w 1s7x 1t0m 1t0n 1u58 1vac 1vad 1wbx 1wby 1wbz 1yn6 1yn7 1z5l 1zhb 1zhn 1zt1 1zt7 2akr 2ckb 2clv 2clz 2fik 2fo4 2fwo 2gaz 2mha 2ol3 2q7y 2qri 2qrs 2qrt 2vaa 2vab 2ve6 2zok 2zol 2zsv 2zsw 3arb 3ard 3are 3arf 3arg 3au1 3buy 3c8k 3cc5 3cch 3ch1 3cpl 3cvh 3dmm 3e6f 3e6h 3ecb 3fol 3fom 3fon 3ftg 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3l3h 3ma7 3nwm 3o8x 3o9w 3p4m 3p4n 3p4o 3p9l 3p9m 3pab 3pqy 3pwu 3qi9 3quk 3qul 3qux 3quy 3quz 3rgv 3rol 3roo 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3ta3 3tbs 3tbt 3tbv 3tbw 3tby 3tn0 3to4 3tvm 3ubx 3vj6 3ws3 3ws6 4apq 4ei5 4elm 4hs3 4huu 4huv 4huw 4hux 4hv8 4iho 4irj 4irs 4l8b 4l8c 4l8d 4mng 4mq7 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zus 4zut 4zuu 4zuv 4zuw 5e8n 5e8o 5e8p 5efi 5fkp 5ivx 5j6g 5j6h 5jwd 5jwe 5sws 5swz
        CD1D1_MOUSE | P11609: 1cd1 1z5l 1zhn 2akr 2fik 2gaz 2q7y 3arb 3ard 3are 3arf 3arg 3au1 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3ma7 3o8x 3o9w 3qi9 3qux 3quy 3quz 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3ta3 3tn0 3to4 3tvm 3ubx 4apq 4ei5 4elm 4irj 4irs 4mng 4mq7 4mx7 4y16 4y2d 4y4f 4y4h 4y4k 5efi 5fkp
        K7N5M3_HUMAN | K7N5M3: 5e6i 5men
        TRBC2_HUMAN | A0A5B9: 1ao7 1bd2 2eyr 2eys 2eyt 3kxf 3o6f 3o8x 3o9w 3qux 3t0e 3ta3 3tvm 4c56 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4udt 4udu 4ww1 4ww2 4wwk 4y16 4y2d 4y4f 4y4h 4y4k 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb
UniProtKB/TrEMBL
        A0A0B4J1J9_M | A0A0B4J1J9: 4y16 4y2d 4y4f 4y4h 4y4k
        A2NTY6_MOUSE | A2NTY6: 2e7l 2icw 2oi9 2pxy 2z31 2z35 3e2h 4y16 4y2d 4y4f 4y4h 4y4k
        K7N5M3_HUMAN | K7N5M3: 4en3 4mji 4mnh 4ndm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZAK)