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(-) Description

Title :  STRUCTURE OF HUMAN CD1D-SULFATIDE
 
Authors :  A. M. Luoma, E. J. Adams
Date :  15 Sep 13  (Deposition) - 18 Dec 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gamma-Delta, T Cell Receptor, Humans, T Cells, Non-Classical, Lipids, Cd1D, Restriction, Immunoglobulin, Major Histocompatibility Complex, Antigen Presentation, Self-Ligands, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Luoma, C. D. Castro, T. Mayassi, L. A. Bembinster, L. Bai, D. Picard, B. Anderson, L. Scharf, J. E. Kung, L. V. Sibener, P. B. Savage, B. Jabri, A. Bendelac, E. J. Adams
Crystal Structure Of V Delta 1 T Cell Receptor In Complex With Cd1D-Sulfatide Shows Mhc-Like Recognition Of A Self-Lipid By Human Gamma Delta T Cells.
Immunity V. 39 1032 2013
PubMed-ID: 24239091  |  Reference-DOI: 10.1016/J.IMMUNI.2013.11.001

(-) Compounds

Molecule 1 - ANTIGEN-PRESENTING GLYCOPROTEIN CD1D, CD1D1 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: HUMAN CD1D ALPHA1,2 DOMAINS FUSED WITH MURINE ALPHA3 DOMAIN
    Gene: CD1D, CD1.2, CD1D1
    Mutation: YES
    Organism Common: HUMAN, MOUSE
    Organism Scientific: HOMO SAPIENS, MUS MUSCULUS
    Organism Taxid: 9606, 10090
    Synonym: R3G1
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: BETA-2-MICROGLOBULIN
    Gene: B2M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CIS1Ligand/Ion(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:23 , THR A:24 , ARG A:25 , ASN A:42 , HOH A:423BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWARECYS A:12 , LEU A:13 , GLN A:14 , LEU A:29 , VAL A:47 , GLN A:62 , PHE A:70 , TYR A:73 , SER A:76 , PHE A:77 , ASP A:80 , PHE A:84 , LEU A:90 , PHE A:118 , LEU A:124 , LEU A:148 , ASP A:151 , TRP A:153 , THR A:154 , THR A:157 , HOH A:402BINDING SITE FOR RESIDUE CIS A 302

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:102 -A:166
2A:206 -A:261
3B:25 -B:80

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:92 -Pro A:93
2Tyr A:212 -Pro A:213
3His B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MQ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MQ7)

(-) Exons   (0, 0)

(no "Exon" information available for 4MQ7)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4mq7a1 A:6-183 automated matches                                                                                                                                            d4mq7a2 A:184-278 automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.....eeeeeeeee..eeeeee.......ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeee..eeeeeee..eeee.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeeee......eeeeeehhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mq7 A   6 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWS 278
                                    15        25        35        45        55        65        75        85        95       105|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        
                                                                                                                             105|                                                                                                                                                                       
                                                                                                                              111                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4mq7b_ B: beta2-microglobulin                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee......eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4mq7 B   1 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRD  98
                                    10        20        30        40        50        60        70        80        90
   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  (3, 3)

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 4MQ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MQ7)

(-) Gene Ontology  (84, 119)

Asymmetric/Biological Unit(hide GO term definitions)

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    His B:31 - Pro B:32   [ RasMol ]  
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  4mq7
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  B2MG_MOUSE | P01887
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  CD1D1_MOUSE | P11609
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  CD1D_HUMAN | P15813
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    Protein-protein Interaction: DIP
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  Q7TMK5_MOUSE | Q7TMK5
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 Related Entries

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

UniProtKB/Swiss-Prot
        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 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zak 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 4mx7 4y16 4y2d 4y4f 4y4h 4y4k 4zak 5efi 5fkp
        CD1D_HUMAN | P15813: 1zt4 2po6 3huj 3sdx 3tzv 3u0p 3vwj 3vwk 4en3 4lhu 4mng 4wo4 4ww2 4wwk
        Q7TMK5_MOUSE | Q7TMK5: 4mng

(-) Related Entries Specified in the PDB File

4mng COMPLEX STRUCTURE OF DP10.7 TCR WITH CD1D-SULFATIDE
4mnh STRUCTURE OF UNLIGANDED DP10.7 TCR