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(-) Description

Title :  PCGF5-RING1B-UBCH5C COMPLEX
 
Authors :  A. M. Taherbhoy, A. G. Cochran
Date :  23 Mar 15  (Deposition) - 15 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  E2, E3, Ring Domain, Ubiquitin Ring E3 Ligase, Ligase-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Taherbhoy, O. W. Huang, A. G. Cochran
Bmi1-Ring1B Is An Autoinhibited Ring E3 Ubiquitin Ligase.
Nat Commun V. 6 7621 2015
PubMed-ID: 26151332  |  Reference-DOI: 10.1038/NCOMMS8621

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D3
    ChainsA, D
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUBE2D3, UBC5C, UBCH5C
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN CARRIER PROTEIN D3, UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3, UBIQUITIN- PROTEIN LIGASE D3
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE RING2
    ChainsB, E
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRING DOMAIN, UNP RESIDUES 1-116
    GeneRNF2, BAP1, DING, HIPI3, RING1B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUNTINGTIN-INTERACTING PROTEIN 2-INTERACTING PROTEIN 3, HIP2-INTERACTING PROTEIN 3, PROTEIN DING, RING FINGER PROTEIN 1B, RING1B, RING FINGER PROTEIN 2, RING FINGER PROTEIN BAP-1
 
Molecule 3 - POLYCOMB GROUP RING FINGER PROTEIN 5
    ChainsC, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRING DOMAIN, UNP RESIDUES 1-109
    GenePCGF5, RNF159
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRING FINGER PROTEIN 159

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)   DEF
Biological Unit 2 (1x)ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:51 , CYS B:54 , CYS B:72 , CYS B:75BINDING SITE FOR RESIDUE ZN B 200
2AC2SOFTWARECYS B:67 , HIS B:69 , CYS B:87 , CYS B:90BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWARECYS E:51 , CYS E:54 , CYS E:72 , CYS E:75BINDING SITE FOR RESIDUE ZN E 201
4AC4SOFTWARECYS E:67 , HIS E:69 , CYS E:87 , CYS E:90BINDING SITE FOR RESIDUE ZN E 202
5AC5SOFTWARECYS C:18 , CYS C:21 , CYS C:39 , CYS C:42BINDING SITE FOR RESIDUE ZN C 201
6AC6SOFTWARECYS C:34 , HIS C:36 , CYS C:53 , CYS C:56BINDING SITE FOR RESIDUE ZN C 202
7AC7SOFTWARECYS F:18 , CYS F:21 , CYS F:39 , CYS F:42BINDING SITE FOR RESIDUE ZN F 201
8AC8SOFTWARECYS F:34 , HIS F:36 , CYS F:53 , CYS F:56BINDING SITE FOR RESIDUE ZN F 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S3O)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:60 -Pro A:61
2Tyr D:60 -Pro D:61
3Arg E:81 -Ser E:82
4Ser E:82 -Gly E:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S3O)

(-) Exons   (0, 0)

(no "Exon" information available for 4S3O)

(-) 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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s3o A   0 GSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhh..............hhhhhhhhhh..........eeee.....eeehhhhhhhhh.............hhh.eeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4s3o B  10 TQPLSKTWELSLYELQRTPQEAITDLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS 116
                                    19        29    ||  40        50        60        70        80 ||     91       101       111     
                                                   34|                                            82|                                
                                                    36                                             84                                

Chain C from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..........eeee....eeeehhhhhhhh...............hhhh.eeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4s3o C   6 KHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQVETNPLEMLRLDNTLEEIIFKLVPGLREQELERESEFWKKN 101
                                    15        25        35        45        55    ||  66        76        86        96     
                                                                                 60|                                       
                                                                                  62                                       

Chain D from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s3o D   0 GSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhh......hhhhhhhhhh..........eeee.....eeehhhhhhhhh..............hhh.eeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4s3o E  10 TQPLSKTWELSLYELQRTPQEAVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPS 116
                                    19        29 ||     47        57        67        77        87        97       107         
                                                31|                                                                            
                                                 40                                                                            

Chain F from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..........eeee....eeeehhhhhhhhh...............hhhh.eeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4s3o F   8 LVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQVHETNPLEMLRLDNTLEEIIFKLVPGLREQELERESEFWKKNK 102
                                    17        27        37        47        57        67        77        87        97     

   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 4S3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S3O)

(-) Gene Ontology  (62, 74)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RING2_HUMAN | Q994962h0d 3gs2 3h8h 3ixs 3rpg 4r8p
        UB2D3_HUMAN | P610771x23 2fuh 3l1z 3rpg 3ugb 4bvu 4r8p 5egg 5ifr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4S3O)