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(-) Description

Title :  CRYSTAL STRUCTURE OF SOPA-TRIM56 COMPLEX
 
Authors :  S. Bhogaraju, I. Dikic
Date :  11 May 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubiquitination, Bacterial Effector, Sopa, Trim56, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Fiskin, S. Bhogaraju, L. Herhaus, S. Kalayil, M. Hahn, I. Dikic
Structural Basis For The Recognition And Degradation Of Hos Trim Proteins By Salmonella Effector Sopa.
Nat Commun V. 8 14004 2017
PubMed-ID: 28084320  |  Reference-DOI: 10.1038/NCOMMS14004

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE SOPA
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SOPA, STM2066
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Synonym: SALMONELLA OUTER PROTEIN A,SECRETED EFFECTOR PROTEIN SOPA
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE TRIM56
    Chains: B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TRIM56, RNF109
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: BINDS TO 2 ZN ATOMS.
    Synonym: RING FINGER PROTEIN 109,TRIPARTITE MOTIF-CONTAINING PROTEIN 56

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:21 , CYS B:24 , CYS B:41 , CYS B:44binding site for residue ZN B 101
2AC2SOFTWARECYS B:36 , HIS B:38 , CYS B:56 , CYS B:59binding site for residue ZN B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JW7)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Lys A:185 -Ala A:186
2Ala A:186 -Gly A:187
3Glu A:188 -Thr A:189
4Pro A:406 -Pro A:407
5Phe B:77 -Phe B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JW7)

(-) Exons   (0, 0)

(no "Exon" information available for 5JW7)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh......hhhhhh.........hhhhhh...........ee.................eee.................eee.......ee..........eee.......ee...........................eeee..eeee.....hhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jw7 A 167 PSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGDIIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQQPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENAVDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVSVLAHPPYTQSALISEWLGPVQERFLEA 428
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426  


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee.....eehhhhhhhhh....ee.....ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5jw7 B  18 FLACKICLEQLRAPKTLPCLHTYCQDCLAQLADGGRVRCPECRETVPVPPEGVASFKTNFF  78
                                    27        37        47        57        67        77
   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 5JW7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JW7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JW7)

(-) Gene Ontology  (18, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:186 - Gly A:187   [ RasMol ]  
    Glu A:188 - Thr A:189   [ RasMol ]  
    Lys A:185 - Ala A:186   [ RasMol ]  
    Phe B:77 - Phe B:78   [ RasMol ]  
    Pro A:406 - Pro A:407   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SOPA_SALTY | Q8ZNR3: 2qyu 2qza 3sy2

(-) Related Entries Specified in the PDB File

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