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(-) Description

Title :  COMPLEX OF TRIM25 RING WITH UBCH5-UB
 
Authors :  K. Rittinger, M. G. Koliopoulos, D. Esposito
Date :  17 Dec 15  (Deposition) - 18 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  E3 Ligase, Ubiquitin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Koliopoulos, D. Esposito, E. Christodoulou, I. A. Taylor, K. Rittinger
Functional Role Of Trim E3 Ligase Oligomerization And Regulation Of Catalytic Activity.
Embo J. V. 35 1204 2016
PubMed-ID: 27154206  |  Reference-DOI: 10.15252/EMBJ.201593741

(-) Compounds

Molecule 1 - E3 UBIQUITIN/ISG15 LIGASE TRIM25
    ChainsA, D
    EC Number6.3.2.-, 2.3.2.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTRIM25, EFP, RNF147, ZNF147
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymESTROGEN-RESPONSIVE FINGER PROTEIN,RING FINGER PROTEIN 147, RING-TYPE E3 UBIQUITIN TRANSFERASE,TRIPARTITE MOTIF-CONTAINING PROTEIN 25,UBIQUITIN/ISG15-CONJUGATING ENZYME TRIM25,ZINC FINGER PROTEIN 147
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 D1
    ChainsB, E
    EC Number2.3.2.23, 2.3.2.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUBE2D1, SFT, UBC5A, UBCH5, UBCH5A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym(E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D1,E2 UBIQUITIN-CONJUGATING ENZYME D1,STIMULATOR OF FE TRANSPORT,SFT,UBC4/5 HOMOLOG,UBCH5,UBIQUITIN CARRIER PROTEIN D1,UBIQUITIN-CONJUGATING ENZYME E2(17)KB 1,UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 1,UBIQUITIN- PROTEIN LIGASE D1
 
Molecule 3 - UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
    ChainsC, F
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymUBIQUITIN CARBOXYL EXTENSION PROTEIN 80

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , CYS A:16 , LYS A:21 , CYS A:33 , CYS A:36binding site for residue ZN A 101
2AC2SOFTWARECYS A:28 , HIS A:30 , CYS A:50 , CYS A:53binding site for residue ZN A 102
3AC3SOFTWARECYS D:28 , HIS D:30 , CYS D:50 , CYS D:53binding site for residue ZN D 101
4AC4SOFTWARECYS D:13 , CYS D:16 , CYS D:33 , CYS D:36binding site for residue ZN D 102
5AC5SOFTWAREHIS E:75 , ASN E:77 , ILE E:78 , ILE E:84 , LEU E:86 , ASP E:117 , PRO E:118 , LEU E:119 , VAL E:120 , ILE E:123 , TYR E:134 , ARG F:74 , GLY F:75binding site for Di-peptide GLY F 76 and LYS E 85

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr B:60 -Pro B:61
2Tyr E:60 -Pro E:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FER)

(-) 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:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...........eee.....eeehhhhhhhhhhh...ee......ee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 5fer A   1 MAELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVQGSPYLCPQCRAVYQARPQLHKNTVLCNVVEQFLQA  79
                                    10        20        30        40        50        60        70         

Chain B from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....eeee.......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fer B   1 MALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKY 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     

Chain C from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5fer C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

Chain D from PDB  Type:PROTEIN  Length:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...........eee.....eeehhhhhhhhhh....ee......ee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 5fer D   3 ELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVQGSPYLCPQCRAVYQARPQLHKNTVLCNVVEQFLQADLA  82
                                    12        22        32        42        52        62        72        82

Chain E from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fer E   1 MALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYA 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain F from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5fer F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

   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 5FER)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (58, 68)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RS27A_BOVIN | P629921aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4m0w 4y1h 4z9s 5bz0 5jqs 5mn9
        TRI25_HUMAN | Q142584cfg 4ltb 5eya
        UB2D1_HUMAN | P516682c4p 2yho 3oj4 3ptf 4ap4 4qpl

(-) Related Entries Specified in the PDB File

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