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(-) Description

Title :  CRYSTAL STRUCTURE OF K48-LINKED DIUBIQUITIN WITH F45W MUTATION IN THE PROXIMAL UNIT
 
Authors :  M. A. Nakasone, P. J. Paukstelis, D. Fushman
Date :  07 Nov 15  (Deposition) - 16 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Ubiquitin Signaling, Multidomain System, Fluorescence Assay, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Nakasone, C. Geng, M. Chojnacki, M. Glickman, P. J. Paukstelis, D. Fushman
Structural Characterization And Practical Fluorescence Applications Of The F45W Ubiquitin Mutant
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYUBIQUITIN-B
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:42 , GLN A:49 , ARG A:72 , ARG B:42 , GLN B:49 , ARG B:72 , HOH B:246binding site for residue SO4 B 101
2AC2SOFTWAREARG C:42 , GLN C:49 , ARG C:72 , ARG D:42 , GLN D:49 , ARG D:72binding site for residue SO4 D 101
3AC3SOFTWAREARG E:42 , GLN E:49 , HOH E:205 , ARG F:42 , GLN F:49binding site for residue SO4 E 101
4AC4SOFTWAREHOH E:208 , HOH E:209binding site for residue SO4 E 102
5AC5SOFTWAREILE C:44 , PHE C:45 , ALA C:46 , GLY C:47 , GLN C:49 , LEU C:50 , LEU C:71 , LEU C:73 , ARG C:74 , GLY C:75 , ILE D:44 , TRP D:45 , ALA D:46 , GLY D:47 , GLN D:49 , LEU D:50 , LEU D:71 , HOH D:212 , HOH D:226binding site for Di-peptide LYS D 48 and GLY C 76
6AC6SOFTWARELEU A:71 , ALA B:46 , ILE E:44 , PHE E:45 , ALA E:46 , GLY E:47 , GLN E:49 , LEU E:50 , LEU E:71 , LEU E:73 , ARG E:74 , GLY E:75 , HOH E:203 , HOH E:207 , HOH E:212 , HOH E:227 , ILE F:44 , TRP F:45 , ALA F:46 , GLY F:47 , GLN F:49 , LEU F:50 , LEU F:71 , LEU F:73binding site for Di-peptide LYS F 48 and GLY E 76

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMZ)

(-) 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:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5emz A  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  5emz B  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                    10        20        30        40        50        60        70    


Chain C from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5emz C  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain D from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  5emz D  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQKESTLHLVLRL 73
                                    10        20        30        40        50        60        70   


Chain E from PDB  Type:PROTEIN  Length:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5emz E  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain F from PDB  Type:PROTEIN  Length:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  5emz F  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQKESTLHLVLRL 73
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
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  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 5EMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 89)

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 Related Entries

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

UniProtKB/Swiss-Prot
        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 5d0m 5dfl 5dk8 5e6j 5edv 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

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