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(-) Description

Title :  STRUCTURE OF UBE2D2:RNF165:UB COMPLEX
 
Authors :  J. D. Wright, C. L. Day, P. D. Mace
Date :  03 Aug 15  (Deposition) - 09 Dec 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Complex, Ubiquitin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Wright, P. D. Mace, C. L. Day
Secondary Ubiquitin-Ring Docking Enhances Arkadia And Ark2C E3 Ligase Activity.
Nat. Struct. Mol. Biol. V. 23 45 2016
PubMed-ID: 26656854  |  Reference-DOI: 10.1038/NSMB.3142

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    Chains: A
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBIQUITIN CARRIER PROTEIN D2,UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2,UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2,UBIQUITIN-PROTEIN LIGASE D2,P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1
 
Molecule 2 - RING FINGER PROTEIN 165
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 255-346
    Gene: RNF165
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - POLYUBIQUITIN-B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-76
    Gene: UBB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:104 , SER A:108 , HOH A:326 , HIS B:68binding site for residue PO4 A 201
2AC2SOFTWARECYS C:312 , HIS C:314 , CYS C:331 , CYS C:334binding site for residue ZN C 401
3AC3SOFTWARECYS C:294 , CYS C:297 , HIS C:317 , CYS C:320binding site for residue ZN C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D0M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5D0M)

(-) 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:147
                                                                                                                                                                                   
               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
                 5d0m A   1 MALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain B 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
                 5d0m B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      


Chain C from PDB  Type:PROTEIN  Length:60
                                                                                            
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh.eeee..............eeee.....eeehhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 5d0m C 258 QNTIERFTFPHKYKEKCTICLSMLGEDVRRLPCAHLFHQLCVDQWLAMSKKCPICRVDIE 339
                                   267   ||  297   ||  309       319       329       339
                                       271|      301|                                   
                                        292       304
   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 5D0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D0M)

(-) Gene Ontology  (113, 129)

Asymmetric/Biological Unit(hide GO term definitions)

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    Tyr A:60 - Pro A:61   [ RasMol ]  
 

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  5d0m
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  RN165_HUMAN | Q6ZSG1
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  UB2D2_HUMAN | P62837
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  UBB_HUMAN | P0CG47
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  6.3.2.19
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 Related Entries

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

UniProtKB/Swiss-Prot
        RN165_HUMAN | Q6ZSG1: 5d0i 5d0k 5ulh 5ulk
        UB2D2_HUMAN | P62837: 1ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 4wz3 5d0k 5d1k 5d1l 5d1m 5edv 5mnj 5ulf 5ulh 5ulk
        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 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 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

(-) Related Entries Specified in the PDB File

5d0i 5d0k