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(-) Description

Title :  CRYSTAL STRUCTURE OF RNF146(RING-WWE)/UBCH5A/ISO-ADPR COMPLEX
 
Authors :  Z. Wang, P. A. Darosa, R. E. Klevit, W. Xu
Date :  23 Jun 14  (Deposition) - 15 Oct 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Protein Poly(Adp-Ribosy)Lation, Ubiquitination, E2/E3 Ubiquitin Ligase, Wnt Signaling, Rnf146, Ubch5A, Iso-Adpr, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. A. Darosa, Z. Wang, X. Jiang, J. N. Pruneda, F. Cong, R. E. Klevit, W. X
Allosteric Activation Of The Rnf146 Ubiquitin Ligase By A Poly(Adp-Ribosyl)Ation Signal.
Nature V. 517 223 2015
PubMed-ID: 25327252  |  Reference-DOI: 10.1038/NATURE13826

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RNF146
    ChainsA, C
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 32-185
    GeneRNF146
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIDUNA, RING FINGER PROTEIN 146
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 D1
    ChainsB, D
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUBE2D1, SFT, UBC5A, UBCH5, UBCH5A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTIMULATOR 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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1V3L2Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1V3L1Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1V3L1Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:61 , TYR A:107 , GLY A:109 , ARG A:110 , TRP A:114 , TYR A:116 , ILE A:139 , TYR A:144 , GLN A:153 , ARG A:161 , ARG A:163 , LYS A:175 , GLY A:179 , HOH A:302 , HOH A:305 , HOH A:306 , HOH A:318 , HOH A:330BINDING SITE FOR RESIDUE V3L A 201
2AC2SOFTWARECYS A:36 , CYS A:39 , CYS A:56 , CYS A:59BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWARECYS A:51 , HIS A:53 , CYS A:70 , CYS A:73BINDING SITE FOR RESIDUE ZN A 203
4AC4SOFTWARELYS C:61 , TYR C:107 , GLY C:109 , ARG C:110 , TRP C:114 , TYR C:116 , ILE C:139 , TYR C:144 , GLN C:153 , ARG C:161 , ARG C:163 , LYS C:175 , GLY C:179 , HOH C:301 , HOH C:303 , HOH C:304 , HOH C:319 , HOH C:320 , HOH C:345BINDING SITE FOR RESIDUE V3L C 201
5AC5SOFTWARECYS C:36 , CYS C:39 , CYS C:56 , CYS C:59BINDING SITE FOR RESIDUE ZN C 202
6AC6SOFTWARECYS C:51 , HIS C:53 , CYS C:70 , CYS C:73BINDING SITE FOR RESIDUE ZN C 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr B:60 -Pro B:61
2Tyr D:60 -Pro D:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QPL)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.....eeehhhhhhhhh.......................hhhhhhhhh.....eeeeeee..eeee.hhhhhhhhhhhhhh...eeeeee..eeeeee....eeee......eeeeeeee......ee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpl A  30 SLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLDKPTLLSPEELKAASRGNGEYAWYYEGRNGWWQYDERTSRELEDAFSKGKKNTEMLIAGFLYVADLENMVQYRRNEHGRRRKIKRDIIDIPKKGVAGLRL 182
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   

Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpl B  -1 HAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138         

Chain C from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.....eeehhhhhhhhh.......................hhhhhhhhhhh...eeeeeee..eeee.hhhhhhhhhhhhhh...eeeeee..eeeeee....eeee.......eeeeeee......ee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpl C  30 SLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLDKPTLLSPEELKAASRGNGEYAWYYEGRNGWWQYDERTSRELEDAFSKGKKNTEMLIAGFLYVADLENMVQYRRNEHGRRRKIKRDIIDIPKKGVAGLRL 182
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   

Chain D from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpl D  -5 HHHHHAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144   

   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 4QPL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 43)

Asymmetric Unit(hide GO term definitions)

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        RN146_MOUSE | Q9CZW61ujr 2rsf
        UB2D1_HUMAN | P516682c4p 2yho 3oj4 3ptf 4ap4 5fer

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