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(-) Description

Title :  CRYSTAL STRUCTURE OF CYLD USP DOMAIN (C596A) IN COMPLEX WITH LYS63-LINKED DIUBIQUITIN
 
Authors :  Y. Sato, S. Fukai
Date :  30 Jul 14  (Deposition) - 11 Feb 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Ubiquitin Protease, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Sato, A. Yamagata, S. Goto-Ito, K. Kubota, S. Fukai
Structures Of Cyld Usp With Met1- Or Lys63-Linked Diubiquitin Reveal Mechanisms For Dual Specificity
Nat. Struct. Mol. Biol. 2015
PubMed: search  |  Reference-DOI: 10.1038/NSMB.2970

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLDI
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: USP DOMAIN, UNP RESIDUES 578-780, LINKER, 850-951
    Gene: CYLD, CYLDA
    Mutation: YES
    Organism Common: ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: CYLD PROTEIN
 
Molecule 2 - UBIQUITIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UBC
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DISTAL UBIQUITIN
 
Molecule 3 - UBIQUITIN
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-72
    Gene: UBC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PROXIMAL UBIQUITIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WXG)

(-) Sites  (0, 0)

(no "Site" information available for 3WXG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WXG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WXG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WXG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WXG)

(-) Exons   (0, 0)

(no "Exon" information available for 3WXG)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..ee.....hhhhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh......eeee.hhh.eeee..ee............hhhhhhhhhhhhh.........eeeee..................eee.hhhh..eeeeeeeeee....eeeeee.......eeeeeeeeeeee...eeeeeeeeehhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhheeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wxg A 577 MGLEVMVGKKKGIQGHYNSAYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQELLRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEEKDPEEFLNILFHHILRVDPLLRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRFGKDFKMFNKIFPSLELDITDLLDQQMELFAVLCIETSHYVAFVKYGSADSAWLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYMCMYQSPTMSLY 885
                                   586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776||     795       805       815       825       835       845       855       865       875       885
                                                                                                                                                                                                                                  777|                                                                                                  
                                                                                                                                                                                                                                   787                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhhhhh.....eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3wxg B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      


Chain C from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee................eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3wxg C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  72
                                    10        20        30        40        50        60        70  


Chain D from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..ee.....hhhhhhhhhhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh......eeeeehhheeeee..ee............hhhhhhhhhhhhh.........eeeee..................eee.hhhh..eeeeeeeeee....eeeeee.......eeeeeeeeeeee...eeeeeeeeehhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhheeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wxg D 577 MGLEVMVGKKKGIQGHYNSAYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQELLRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEEKDPEEFLNILFHHILRVDPLLRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRFGKDFKMFNKIFPSLELDITDLLDQQMELFAVLCIETSHYVAFVKYGSADSAWLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYMCMYQSPTMSLY 885
                                   586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776||     795       805       815       825       835       845       855       865       875       885
                                                                                                                                                                                                                                  777|                                                                                                  
                                                                                                                                                                                                                                   787                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3wxg E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      


Chain F from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee................eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3wxg F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  72
                                    10        20        30        40        50        60        70
   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 3WXG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WXG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WXG)

(-) Gene Ontology  (25, 26)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBC_MOUSE | P0CG50: 1cmx 1gjz 1ud7 1uzx 2znv 3a1q 3a9j 3a9k 3vht 3wwq 4nql
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(-) Related Entries Specified in the PDB File

3wxe 3wxf