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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UAF1/WDR20/USP12 COMPLEX
 
Authors :  H. Li, A. D. D'Andrea, N. Zheng
Date :  18 May 16  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Wd40 Repeat Domain, Wdr20, Usp12, Uaf1, Wdr48, Deubiquitinating Enzyme, Ubiquitin-Specific Protease, Usp1-Associated Factor 1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, K. S. Lim, H. Kim, T. R. Hinds, U. Jo, H. Mao, C. E. Weller, J. Sun, C. Chatterjee, A. D. D'Andrea, N. Zheng
Allosteric Activation Of Ubiquitin-Specific Proteases By Beta-Propeller Proteins Uaf1 And Wdr20.
Mol. Cell V. 63 249 2016
PubMed-ID: 27373336  |  Reference-DOI: 10.1016/J.MOLCEL.2016.05.031

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 12
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Taxid: 274590
    Fragment: RESIDUES 16-370
    Gene: USP12, UBH1, USP12L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME 12,UBIQUITIN THIOESTERASE 12, UBIQUITIN-HYDROLYZING ENZYME 1,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 12
 
Molecule 2 - WD REPEAT-CONTAINING PROTEIN 48
    Chains: B
    Engineered: YES
    Expression System: BACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Taxid: 274590
    Fragment: RESIDUES 1-563
    Gene: WDR48, KIAA1449, UAF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: USP1-ASSOCIATED FACTOR 1,WD REPEAT ENDOSOMAL PROTEIN,P80
 
Molecule 3 - WD REPEAT-CONTAINING PROTEIN 20
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Gene: WDR20
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN DMR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:186 , CYS A:189 , CYS A:233 , CYS A:236binding site for residue ZN A 401
2AC2SOFTWARELYS B:168 , ARG B:193 , LYS B:202 , LYS B:205binding site for residue PO4 B 601
3AC3SOFTWAREASP C:63 , TYR C:78 , TYR C:315 , LEU C:542 , GLU C:543 , ASP C:544 , HOH C:715binding site for residue TAM C 601

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:186 -A:189
2A:186 -A:236
3A:186 -A:233
4A:189 -A:236
5A:189 -A:233

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K1C)

(-) Exons   (0, 0)

(no "Exon" information available for 5K1C)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee.....eeeeeeee.eeee.....eehhhhhhhhh.eeeehhhhheee....eee.eeeeeeeee...eeeeee..ee........ee....ee...ee...............eeeeeeeeee.......eeeeeee....eeee....eee.hhhhhhhhh............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k1c A  37 HYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYSLLTCLADLFHSIATQVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYGLTSDISKNSESGYILFYQSRD 370
                                    46        56        66   ||   84        94|      109       119       129       139       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  
                                                            70|             94|                                            147|                                                                                                                                                                                                           
                                                             79             100                                             167                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........eeeee........eeee....eee............eee......eeeeeee....eeeeee....eeeee....eeeeee......eeeeeeehhh.eeeeee....eeeeehhhhhh...................eeeeee......eeeee....eeee......eeeee........eeee.....eeeee.....eeeee....eeeeee......eeeeee.....eeeeee...eeeeee.......eeeee....eeeeee........eeeeee....eeeee...................ee.....eeeeee.....eeeeee.....eeee....eeeee....hhhhhhhhh..........eee.....eeeee........eeehhhhh.........eeehhhhhhhhhh..hhhhh...............eeee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k1c B  14 KVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIASMEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQIFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHTDNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTDLRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLKGIHNFNPITPLCTQPDQVIKGGASIIQCHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKRFKMVYVPNWFSVDLKTGMLTITLDESDCFAAWVSAKDAGFSSPDGSDPKLNLGGLLLQALLEYWPRTHENQKGNGYFQVPPHTPVIFGEAGGRTLFRLLCRDSGGETESMLLNETVPQWVIDITVDKNM 559
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       344       354       364       374       384       394       404       414       424       434       444       454       464       474   ||||504       514       524       534       544       554     
                                                                                                                                                                                                                                                                                                                                                        332|                                                                                                                                   478|||                                                          
                                                                                                                                                                                                                                                                                                                                                         344                                                                                                                                    497||                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 498|                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  501                                                          


Chain C from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee..eeeee.hhhh..................eeeee........eeeeeee..eeeeee.......................eeeeeeeeeee....eeeeeee....eeee.....................eeeeee......eeeeee...eeeeee...........eeeeeee..eeeeee.........eeeee....eeeeee.....eeeeee...eeeeee....eeeeeee.........ee.....eeeee....eeeeee....eeeeeee.....eeeeee.hhhh.....eeeeeee...eeeeeeehhhhhh..................ee...eeee.....eeeeeee..eeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k1c C   1 MATEGGGNEIKTQFTTREGLYKLLPHSEYSRPNRVPFNSQGSNPVRVSFVNLNDQSGNGDRLCFNVGRELYFYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNHLTATAESVSLLVGFSAGQVQLIDPIKKETSKLFNEERLIDKSRVTCVKWVPGSESLFLVAHSSGNMYLYNVEHTCGTTAPHYQLLKQGESFAVHTCKSKSTRNPLLKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSVELHGTMKSYFGGLLCVCWSPDGKYIVTGGEDDLVTVWSFVDCRVIARGHGHKSWVSVVAFDPYTTSVSVTYRFGSVGQDTQLCLWDLTEDILFPHQPLLGTPLCPRMEDVPLLEPLICKKIAHERLTVLIFLEDCIVTACQEGFICTWGRPGKVVSFN 568
                                  ||13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313    || 367       377       387      |511       521       531       541       551       561       
                                  7|                                                                                                                                                                                                                                                                                                                318|                            394|                                                           
                                  11                                                                                                                                                                                                                                                                                                                 363                             509
   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 5K1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K1C)

(-) Gene Ontology  (30, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBP12_HUMAN | O75317: 5k16 5k1a 5k1b 5l8w
        WDR20_HUMAN | Q8TBZ3: 5k19
        WDR48_HUMAN | Q8TAF3: 5cvl 5cvn 5cvo 5k1a 5k1b 5l8e 5l8w

(-) Related Entries Specified in the PDB File

5k16 5k19 5k1a 5k1b