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(-) Description

Title :  E3 UBIQUITIN-PROTEIN LIGASE RNF8 IN COMPLEX WITH UBIQUITIN-CONJUGATING ENZYME E2 N AND POLYUBIQUITIN-B
 
Authors :  C. D. Hodge, R. A. Edwards, J. N. M. Glover
Date :  23 Sep 14  (Deposition) - 30 Sep 15  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  8.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  E3 Ligase, E2 Conjugating Enzyme, Ubiquitination, Coiled Coil, Ligase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Hodge, I. H. Ismail, R. A. Edwards, G. L. Hura, A. T. Xiao, J. A. Tainer, M. J. Hendzel, J. N. Glover
Rnf8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential For Dna Double Strand Break Signaling And Brca1 Tumor Suppressor Recruitment.
J. Biol. Chem. V. 291 9396 2016
PubMed-ID: 26903517  |  Reference-DOI: 10.1074/JBC.M116.715698

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 N
    Chains: B, E, H, K
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-152
    Gene: UBE2N, BLU
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME,UBC13,UBCH13, UBIQUITIN CARRIER PROTEIN N,UBIQUITIN-PROTEIN LIGASE N
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE RNF8
    Chains: C, D, I, J
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 345-485
    Gene: RNF8, KIAA0646
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HRNF8,RING FINGER PROTEIN 8
 
Molecule 3 - POLYUBIQUITIN-B
    Chains: A, F, G, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET47B+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-76
    Gene: UBB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL

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  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:418 , HIS C:420 , CYS C:437 , CYS C:440binding site for residue ZN C 501
2AC2SOFTWARECYS C:403 , CYS C:406 , CYS C:423 , CYS C:426binding site for residue ZN C 502
3AC3SOFTWARECYS D:418 , HIS D:420 , CYS D:437 , CYS D:440binding site for residue ZN D 501
4AC4SOFTWARECYS D:403 , CYS D:406 , CYS D:423 , CYS D:426binding site for residue ZN D 502
5AC5SOFTWARECYS I:418 , HIS I:420 , CYS I:437 , CYS I:440binding site for residue ZN I 501
6AC6SOFTWARECYS I:403 , CYS I:406 , CYS I:423 , CYS I:426binding site for residue ZN I 502
7AC7SOFTWARECYS J:418 , HIS J:420 , CYS J:437 , CYS J:440binding site for residue ZN J 501
8AC8SOFTWARECYS J:403 , CYS J:406 , CYS J:423 , CYS J:426binding site for residue ZN J 502
9AC9SOFTWAREPRO E:27 , ASP E:28 , ASN E:31 , ALA E:32 , ARG E:33 , PHE E:35 , HIS E:36 , GLU E:55 , LEU E:56 , THR E:73 , ILE E:75 , TRP E:143 , TYR E:147binding site for Di-peptide TYR E 34 and LYS E 74

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr B:62 -Pro B:63
2Tyr E:62 -Pro E:63
3Tyr H:62 -Pro H:63
4Tyr K:62 -Pro K:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WHV)

(-) 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:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4whv A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70 


Chain B from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv B   4 LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeee....eeehhhhhhhh...............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv C 345 QEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERK 480
                                   354       364       374       384       394       404       414       424       434       444       454       464       474      


Chain D from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeee....eeehhhhhhhhhhh............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv D 342 PEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERK 480
                                   351       361       371       381       391       401       411       421       431       441       451       461       471         


Chain E from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv E   4 LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain F from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4whv F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70 


Chain G from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4whv G   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70 


Chain H from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv H   4 LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain I from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.............eeee....eeehhhhhhhh...............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4whv I 380 EKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERK 480
                                   389       399       409       419       429       439       449       459       469       479 


Chain J from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...............eeee....eeehhhhhhhhhhh............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4whv J 380 EKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERK 480
                                   389       399       409       419       429       439       449       459       469       479 


Chain K from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whv K   4 LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain L from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4whv L   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
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  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 4WHV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (142, 170)

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  4whv
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  RNF8_HUMAN | O76064
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  UBB_HUMAN | P0CG47
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  UBE2N_HUMAN | P61088
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNF8_HUMAN | O76064: 2csw 2pie 4ayc 4orh
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5
        UBE2N_HUMAN | P61088: 1j7d 2c2v 3hct 3hcu 3von 3w31 4dhi 4dhj 4dhz 4ip3 4nr3 4nrg 4nri 4onl 4onm 4onn 4orh 4tkp 5ait 5aiu 5eya

(-) Related Entries Specified in the PDB File

4orh