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(-) Description

Title :  MOLECULAR BASIS FOR ABROGATION OF ACTIVATION OF PRO-INFLAMMATORY CYTOKINES
 
Authors :  H. Ru, X. Ni, C. Crowley, L. Zhao, W. Ding, L. -W. Hung, N. Shaw, G. Cheng, Z
Date :  19 Feb 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,D,E,F  (1x)
Biol. Unit 2:  B,G  (2x)
Biol. Unit 3:  C,H  (2x)
Keywords :  Ob Fold, Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ru, X. Ni, L. Zhao, C. Crowley, W. Ding, L. -W. Hung, N. Shaw, G. Cheng, Z. -J. Liu
Structural Basis For Termination Of Aim2-Mediated Signaling By P202
Cell Res. V. 23 855 2013
PubMed-ID: 23567559  |  Reference-DOI: 10.1038/CR.2013.52

(-) Compounds

Molecule 1 - INTERFERON-ACTIVABLE PROTEIN 202
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HINA DOMAIN, UNP RESIDUES 46-242
    Gene: IFI202A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IFI-202, INTERFERON-INDUCIBLE PROTEIN P202, LUPUS SUSCEPTIBILITY PROTEIN P202
 
Molecule 2 - DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
    Chains: E, F, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A  DEF  
Biological Unit 2 (2x):  B    G 
Biological Unit 3 (2x):   C    H

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4JBK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JBK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr B:3 -Pro B:4
2Asn D:150 -Glu D:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JBK)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains d4jbka1 A:3-112 automated matches                                                                             d4jbka2 A:113-199 automated matches                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee...eeeeeeee.............eeeeeee..eeeeeee.hhhhh.......eeeee.eeee..eeee....eeee.........hhhhhhhhhh..hhhhhh......eeeeeeeeeeeee....eeeeee....eeeeee.........eeeeeeeeee....eeee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jbk A   3 TPKKNISKGAVLHEKPMTVMVLTATEPFNYKEGKENMFHATVATESQYYRVKVFNMDLKEKFTENKFITISKYFNSSGILEINETATVSEAAPNQMFEVPKNIIRSAKETLKISKIKELDSGTLIYGVFAVEKKKVNDKSITFKIKDNEDNIKVVWDKEQHNINKLQLFSFHLRKGNGKPILHSGNHSFIKG 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   ||  177       187       197  
                                                                                                                                                                                             166|                           
                                                                                                                                                                                              172                           


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains d4jbkb1 B:3-112 automated matches                                                                             d4jbkb2 B:113-199 automated matches                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...eeeeeeee.............eeeeee....eeeeee.hhhhh.......eeeee.eeee..eeee....eeee.hhhhh...hhhhhhhhhh..hhhhhh......eeeeeeeeeeeee....eeeeee....eeeeee......eeeeeeeeee......eee.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jbk B   3 TPKKNISKGAVLHEKPMTVMVLTATEPFNYKEGKENMFHATVATESQYYRVKVFNMDLKEKFTENKFITISKYFNSSGILEINETATVSEAAPNQMFEVPKNIIRSAKETLKISKIKELDSGTLIYGVFAVEKKKVNDKSITFKIKDNEDNIKVVWDKEKGDKLQLFSFHLRKGNGKPILHSGNHSFIKG 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       169       179       189       199
                                                                                                                                                                                       160|                               
                                                                                                                                                                                        168                               


Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains d4jbkc1 C:3-112 automated matches                                                                             d4jbkc2 C:113-199 automated matches                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...eeeeeeee.............eeeeee....eeeeee.hhhhh.......eeeee.eeee..eeee....eeee.........hhhhhhhhhh..hhhhhh......eeeeeeeeeeeee....eeeeee....eeeeee....eeeeeeeeee......eee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jbk C   3 TPKKNISKGAVLHEKPMTVMVLTATEPFNYKEGKENMFHATVATESQYYRVKVFNMDLKEKFTENKFITISKYFNSSGILEINETATVSEAAPNQMFEVPKNIIRSAKETLKISKIKELDSGTLIYGVFAVEKKKVNDKSITFKIKDNEDNIKVVWDKEDKLQLFSFHLRKGNGKPILHSGNHSFIKG 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       171       181       191        
                                                                                                                                                                                        161|                            
                                                                                                                                                                                         171                            


Chain D from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains d4jbkd1 D:3-112 automated matches                                                                             d4jbkd2 D:113-199 automated matches                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...eeeeeeee.............eeeeeee..eeeeeee.hhhhh.......eeeee.eeee..eeee....eeee.........hhhhhhhhhh..hhhhhh......eeee..eeeeeee....eeeeeee..eeeeeee........eeeeee.....eee.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jbk D   3 TPKKNISKGAVLHEKPMTVMVLTATEPFNYKEGKENMFHATVATESQYYRVKVFNMDLKEKFTENKFITISKYFNSSGILEINETATVSEAAPNQMFEVPKNIIRSAKETLKISKIKELDSGTLIYGVFAVEKKKVNDKSITFKIKDNEDNIKVVWDKEQNINQLFSFHLRNGKPILHSGNHSFIKG 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162| ||   180||     192       
                                                                                                                                                                                         162| ||    181|               
                                                                                                                                                                                          164 ||     184               
                                                                                                                                                                                            166|                       
                                                                                                                                                                                             174                       


Chain E from PDB  Type:DNA  Length:14
                                              
                 4jbk E   1 GGAATTATAATTCC  14
                                    10    


Chain F from PDB  Type:DNA  Length:14
                                              
                 4jbk F   1 GGAATTATAATTCC  14
                                    10    


Chain G from PDB  Type:DNA  Length:14
                                              
                 4jbk G   1 GGAATTATAATTCC  14
                                    10    


Chain H from PDB  Type:DNA  Length:14
                                              
                 4jbk H   1 GGAATTATAATTCC  14
                                    10
   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  (1, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Fold: OB-fold (1179)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn D:150 - Glu D:151   [ RasMol ]  
    Thr B:3 - Pro B:4   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        IFI2_MOUSE | Q9R002: 4jbj 4l5q 4l5r 4l5s 4l5t 4lnq

(-) Related Entries Specified in the PDB File

4jbj UNLIGANDED P202A
4jbm