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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CD1D IN COMPLEX WITH THE P99P LIPOPEPTIDE
 
Authors :  E. Girardi, J. Wang, D. M. Zajonc
Date :  23 Oct 15  (Deposition) - 30 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cd1D, Lipopeptide, Alpha-Helical Peptide, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Girardi, J. Wang, D. M. Zajonc
Structure Of An Alpha-Helical Peptide And Lipopeptide Bound To The Nonclassical Major Histocompatibility Complex (Mhc) Class I Molecule Cd1D.
J. Biol. Chem. V. 291 10677 2016
PubMed-ID: 27006394  |  Reference-DOI: 10.1074/JBC.M115.702118

(-) Compounds

Molecule 1 - ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: SF9
    Expression System Taxid: 7108
    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 Strain: SF9
    Expression System Taxid: 7108
    Gene: B2M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - P99P
    Chains: C
    Engineered: YES
    Organism Scientific: MUS
    Organism Taxid: 10088
    Other Details: PALMITATE RESIDUE COVALENTLY LINKED TO LYS 12
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 13)

Asymmetric/Biological Unit (8, 13)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CIT1Ligand/IonCITRIC ACID
3FUC1Ligand/IonALPHA-L-FUCOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NA1Ligand/IonSODIUM ION
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7OCA1Ligand/IonOCTANOIC ACID (CAPRYLIC ACID)
8PLM1Ligand/IonPALMITIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLN A:14 , SER A:28 , TRP A:40 , PHE A:70 , TYR A:73 , NA A:311 , PLM C:101binding site for residue CIT A 310
2AC2SOFTWARETHR A:26 , TRP A:40 , ARG A:74 , CIT A:310binding site for residue NA A 311
3AC3SOFTWARETYR A:73 , THR A:159 , CIT A:310 , LYS C:7binding site for residue PLM C 101
4AC4SOFTWARETRP A:133 , ILE C:4binding site for residue OCA C 102
5AC5SOFTWAREALA A:19 , ASN A:20 , TRP A:23binding site for Mono-Saccharide NAG A 309 bound to ASN A 20
6AC6SOFTWARETRP A:23 , SER A:24 , ASN A:42binding site for Poly-Saccharide residues NAG A 301 through NAG A 302 bound to ASN A 42
7AC7SOFTWARELYS A:57 , SER A:114 , TRP A:129 , GLY A:130 , THR A:131 , GLN A:161 , ASN A:165 , GLU A:177 , ALA A:178 , LYS A:180 , SER A:181 , HOH A:417 , ASN B:42 , GLY B:43 , THR B:77binding site for Poly-Saccharide residues NAG A 303 through MAN A 308 bound to ASN A 165

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:168
2A:208 -A:263
3B:25 -B:80

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:94 -Pro A:95
2Tyr A:214 -Pro A:215
3His B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EFI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EFI)

(-) Exons   (0, 0)

(no "Exon" information available for 5EFI)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..eeeeeeeeee..eeeeee.......ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee..eeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeehhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5efi A   6 KNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMDYPIEIQLSAGCEMYASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVDGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYW 279
                                    15        25        35        45        55        65        75        85  ||    99       112       122       132       142       152       162       172       182       192   ||  206       216       226       236       246       256       266       276   
                                                                                                             88|           107|                                                                                  196|                                                                              
                                                                                                              93            111                                                                                   201                                                                              


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               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
                 5efi B   1 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM  99
                                    10        20        30        40        50        60        70        80        90         


Chain C from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 5efi C   0 DFHHIREKGNHWKNFL  15
                                     9
   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 5EFI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EFI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EFI)

(-) Gene Ontology  (74, 83)

Asymmetric/Biological Unit(hide GO term definitions)

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  CD1D1_MOUSE | P11609
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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 4mq7 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zus 4zut 4zuu 4zuv 4zuw 5e8n 5e8o 5e8p 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 4zak 5fkp

(-) Related Entries Specified in the PDB File

5fkp 5FKP CONTAINS THE SAME STRUCTURE COMPLEXED WITH THE P99 PEPTIDE