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(-) Description

Title :  CRYSTAL STRUCTURE OF RNF8 BOUND TO THE UBC13/MMS2 HETERODIMER
 
Authors :  S. J. Campbell, R. A. Edwards, J. N. M. Glover
Date :  11 Feb 14  (Deposition) - 26 Feb 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.80
Chains :  Asym. Unit :  A,B,C,E,F,G,H,I,J,K,L
Biol. Unit 1:  I,J,K,L  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  A,B,C  (1x)
Keywords :  Coiled-Coil, E3 Ubiquitin Ligase, Ubiquitin, Protein Binding-Ligase, Protein Binding-Ligase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Campbell, R. A. Edwards, C. C. Leung, D. Neculai, C. D. Hodge, S. Dhe-Paganon, J. N. Glover
Molecular Insights Into The Function Of Ring Finger (Rnf)-Containing Proteins Hrnf8 And Hrnf168 In Ubc13/Mms2-Dependent Ubiquitylation.
J. Biol. Chem. V. 287 23900 2012
PubMed-ID: 22589545  |  Reference-DOI: 10.1074/JBC.M112.359653

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
    Chains: A, E, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21 GOLD
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MMS2, UBE2V2, UEV2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DDVIT 1, ENTEROCYTE DIFFERENTIATION-ASSOCIATED FACTOR 1, EDAF-1, ENTEROCYTE DIFFERENTIATION-PROMOTING FACTOR 1, EDPF-1, MMS2 HOMOLOG, VITAMIN D3-INDUCIBLE PROTEIN
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 N
    Chains: B, F, J
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21 GOLD
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: UBE2N, BLU
    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 3 - E3 UBIQUITIN-PROTEIN LIGASE RNF8
    Chains: C, G, H, K, L
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21 GOLD
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RNF8, KIAA0646
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HRNF8, RING FINGER PROTEIN 8

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric Unit : ABCEFGHIJKL
Biological Unit 1 (1x):        IJKL
Biological Unit 2 (1x):    EFGH    
Biological Unit 3 (1x): ABC        

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1ZN10Ligand/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
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS C:418 , HIS C:420 , CYS C:437 , CYS C:440BINDING SITE FOR RESIDUE ZN C 501
02AC2SOFTWARECYS C:403 , CYS C:406 , CYS C:423 , CYS C:426BINDING SITE FOR RESIDUE ZN C 502
03AC3SOFTWARECYS G:418 , HIS G:420 , CYS G:437 , CYS G:440BINDING SITE FOR RESIDUE ZN G 501
04AC4SOFTWARECYS G:403 , CYS G:406 , CYS G:423 , CYS G:426BINDING SITE FOR RESIDUE ZN G 502
05AC5SOFTWARECYS H:418 , HIS H:420 , CYS H:437 , CYS H:440BINDING SITE FOR RESIDUE ZN H 501
06AC6SOFTWARECYS H:403 , CYS H:406 , CYS H:423 , CYS H:426BINDING SITE FOR RESIDUE ZN H 502
07AC7SOFTWARECYS K:418 , HIS K:420 , CYS K:437 , CYS K:440BINDING SITE FOR RESIDUE ZN K 501
08AC8SOFTWARECYS K:403 , CYS K:406 , CYS K:423 , CYS K:426BINDING SITE FOR RESIDUE ZN K 502
09AC9SOFTWARECYS L:418 , HIS L:420 , CYS L:437 , CYS L:440BINDING SITE FOR RESIDUE ZN L 501
10BC1SOFTWARECYS L:403 , CYS L:406 , CYS L:423 , CYS L:426BINDING SITE FOR RESIDUE ZN L 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:73 -Pro A:74
2Tyr B:62 -Pro B:63
3Tyr E:73 -Pro E:74
4Tyr F:62 -Pro F:63
5Tyr I:73 -Pro I:74
6Tyr J:62 -Pro J:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ORH)

(-) 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:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orh A   6 GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYN 144
                                    15        25        35        45        55        65        75        85        95       105       115       125       135         


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               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
                 4orh B   3 GLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...............eeee....eeehhhhhhhhhhh............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4orh C 392 HMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKR 483
                                   401       411       421       431       441       451       461       471       481  


Chain E from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4orh E   7 VKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYN 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        


Chain F from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               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
                 4orh F   3 GLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        


Chain G from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee....eeehhhhhhhh...............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orh G 345 QEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKR 483
                                   354       364       374       384       394       404       414       424       434       444       454       464       474         


Chain H from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeee....eeehhhhhhhhhhh............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orh H 342 PEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKR 483
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481  


Chain I from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4orh I   7 VKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYN 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        


Chain J from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               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
                 4orh J   3 GLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        


Chain K from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee....eeehhhhhhhh...............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orh K 345 QEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKR 483
                                   354       364       374       384       394       404       414       424       434       444       454       464       474         


Chain L from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................eeee....eeehhhhhhhhhhh............eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orh L 342 PEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNLSSEVKERRIVLIRERKAKR 483
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 4ORH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 105)

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  4orh
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  UB2V2_HUMAN | Q15819
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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 4whv
        UB2V2_HUMAN | Q15819: 1j74 1j7d 1zgu 3von 4nr3 4nrg 4nri 4onl 4onm 4onn 5ait
        UBE2N_HUMAN | P61088: 1j7d 2c2v 3hct 3hcu 3von 3w31 4dhi 4dhj 4dhz 4ip3 4nr3 4nrg 4nri 4onl 4onm 4onn 4tkp 4whv 5ait 5aiu 5eya

(-) Related Entries Specified in the PDB File

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