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(-) Description

Title :  CRYSTAL STRUCTURE OF COWPOX VIRUS CPXV018 (OMCP) BOUND TO HUMAN NKG2D
 
Authors :  E. Lazear, C. A. Nelson, D. H. Fremont, Center For Structural Genomi Infectious Diseases (Csgid)
Date :  17 Apr 14  (Deposition) - 21 May 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Secreted Viral Protein, Immune Evasion, Orthopoxvirus, Mhc-Like Fold, Nk Cell Receptor Ligand, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Lazear, M. Sun, C. A. Nelson, J. A. Campbell, L. N. Carayannopoulos, A. R. French, D. H. Fremont, Center For Structural Genomics Of Infectious Diseases (Csgid)
Cowpox Virus Omcp Antagonizes Nkg2D Via An Unexpected Binding Orientation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 93-215
    Gene: KLRK1, D12S2489E, NKG2D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY K MEMBER 1,NK CELL RECEPTOR D,NKG2-D-ACTIVATING NK RECEPTOR
 
Molecule 2 - CPXV018 PROTEIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 20-168
    Gene: CPXV018 CDS
    Mutation: YES
    Organism Common: CPV
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4PDC)

(-) Sites  (0, 0)

(no "Site" information available for 4PDC)

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:96 -A:105
2A:99 -A:110
3A:127 -A:211
4A:189 -A:203
5B:96 -B:105
6B:99 -B:110
7B:127 -B:211
8B:189 -B:203
9C:96 -C:105
10C:99 -C:110
11C:127 -C:211
12C:189 -C:203
13D:96 -D:105
14D:99 -D:110
15D:127 -D:211
16D:189 -D:203
17E:83 -E:133
18F:83 -F:133

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:97 -Pro A:98
2Ser A:194 -Ser A:195
3Gly B:97 -Pro B:98
4Ser B:194 -Ser B:195
5Gly C:97 -Pro C:98
6Ser C:194 -Ser C:195
7Gly D:97 -Pro D:98
8Ser D:194 -Ser D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PDC)

(-) Sequences/Alignments

Asymmetric 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eee..eeeeeeeeeehhhhhhhhhhh...ee........hhhhhhh...ee..eee......eee...........eee......eeeee...eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdc A  93 ESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   102       112       122       132       142       152       162       172       182       192       202       212   


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eee..eeeeeeeeeehhhhhhhhhhh...ee........hhhhhhh...eeeeeee......eee...........eee......eeeee...eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdc B  94 SYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   103       113       123       133       143       153       163       173       183       193       203       213  


Chain C from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eee..eeeeeeeeeehhhhhhhhhhh...ee........hhhhhhh...eeeeeeee....eeee...........eee......eeeee...eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdc C  93 ESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   102       112       122       132       142       152       162       172       182       192       202       212   


Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eee..eeeeeeeeeehhhhhhhhhhhh..ee........hhhhhhh...eeeeeee......eee...........eee......eeeee...eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdc D  93 ESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   102       112       122       132       142       152       162       172       182       192       202       212   


Chain E from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeee...eeeee....eee.hhhhh...hhhhhhhhhhhhhhhh.........eeeeeeeeeeeee..eeeeeeeeee..eee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pdc E   0 GHKLAFNFNLEINGSDTHSTVDVDLDDSQIITFDGKDIRPTIPFMIGDEIFLPFYKNVFSEFFSLFRRVPTSTPYEDLTYFYECDYTDNKSTFDQDYLYNGEEYTVKTQEATNKNMWLTTSEFRLKKWFDGEDCIMHLRSLVRKMEDSKR 149
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149


Chain F from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeee..eeeeee....eee.hhhhh...hhhhhhhhhhhhhhhh..........eeeeeeeeeeee..eeeeeeeeee..eee.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pdc F   0 GHKLAFNFNLEINGSDTHSTVDVDLDDSQIITFDGKDIRPTIPFMIGDEIFLPFYKNVFSEFFSLFRRVPTSTPYEDLTYFYECDYTDNKSTFDQDYLYNGEEYTVKTQEATNKNMWLTTSEFRLKKWFDGEDCIMHLRSLVRKMEDSKR 149
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
   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 4PDC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:97 - Pro A:98   [ RasMol ]  
    Gly B:97 - Pro B:98   [ RasMol ]  
    Gly C:97 - Pro C:98   [ RasMol ]  
    Gly D:97 - Pro D:98   [ RasMol ]  
    Ser A:194 - Ser A:195   [ RasMol ]  
    Ser B:194 - Ser B:195   [ RasMol ]  
    Ser C:194 - Ser C:195   [ RasMol ]  
    Ser D:194 - Ser D:195   [ RasMol ]  
 
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  Q8QN43_COWPX | Q8QN43
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 Related Entries

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

UniProtKB/Swiss-Prot
        NKG2D_HUMAN | P26718: 1hyr 1kcg 1mpu 4s0u
UniProtKB/TrEMBL
        Q8QN43_COWPX | Q8QN43: 4ffe

(-) Related Entries Specified in the PDB File

1hyr HUMAN NKG2D IN COMPLEX WITH MIC-A
1jsk MOUSE NKG2D IN COMPLEX WITH RAE-1BETA
1kcg HUMAN NKG2D IN COMPLEX WITH ULBP3 RELATED ID: CSGID-IDP00259 RELATED DB: TARGETTRACK
1mpu 1MPU IS THE STRUCTURE OF FREE HUMAN NKG2D IMMUNORECEPTOR.
4ffe 4FFE IS THE STRUCTURE OF FREE COWPOX VIRUS CPXV018 (OMCP)