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(-) Description

Title :  STRUCTURE OF LYS33-LINKED DIUB
 
Authors :  M. A. Michel, P. R. Elliott, K. N. Swatek, M. Simicek, J. N. Pruneda, J. L. S. M. V. Freund, D. Komander
Date :  19 Jan 15  (Deposition) - 25 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  G,H  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  C,D  (1x)
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Michel, P. R. Elliott, K. N. Swatek, M. Simicek, J. N. Pruneda, J. L. Wagstaff, S. M. V. Freund, D. Komander
Assembly And Specific Recognition Of K29- And K33-Linked Polyubiquitin.
Mol. Cell V. 58 95 2015
PubMed-ID: 25752577  |  Reference-DOI: 10.1016/J.MOLCEL.2015.01.042

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTAII
    Expression System Vector: PET17
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: ISOPEPTIDE LINKAGES BETWEEN A76 C AND B33 NZ, C76 C AND D33 NZ, E76 C AND F33 NZ
    Synonym: POLYUBIQUITIN-C

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):       GH
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):   CD    

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:8 , HIS A:68 , HOH A:2001 , ILE D:44 , GLY D:47 , HOH D:2016BINDING SITE FOR RESIDUE GOL D1076
02AC2SOFTWAREGLY B:47 , HIS B:68 , LYS C:6 , LEU C:8 , HIS C:68BINDING SITE FOR RESIDUE GOL B1076
03AC3SOFTWARELYS D:29 , HOH D:2009BINDING SITE FOR RESIDUE GOL D1077
04AC4SOFTWAREARG C:42 , GLN C:49 , ARG E:42 , ARG E:72BINDING SITE FOR RESIDUE GOL E1077
05AC5SOFTWARELYS F:6 , THR F:66 , HIS F:68 , LEU G:8BINDING SITE FOR RESIDUE GOL F1075
06AC6SOFTWARELYS B:6 , HIS B:68BINDING SITE FOR RESIDUE GOL B1077
07AC7SOFTWARELYS D:6 , HIS D:68BINDING SITE FOR RESIDUE GOL D1078
08AC8SOFTWAREARG A:72 , GLU F:16 , LYS F:33BINDING SITE FOR RESIDUE GOL A1077
09AC9SOFTWAREGLU D:16 , ARG G:72BINDING SITE FOR RESIDUE GOL D1079
10BC1SOFTWAREMET C:1 , HOH C:2001 , ARG E:11 , ARG F:42BINDING SITE FOR RESIDUE SO4 C1077
11BC2SOFTWARELYS D:48 , ARG D:54 , TYR D:59 , LYS G:63BINDING SITE FOR RESIDUE SO4 D1080
12BC3SOFTWAREARG A:11 , ARG B:42 , GLN B:49 , ARG B:72BINDING SITE FOR RESIDUE SO4 B1078
13BC4SOFTWAREARG A:72 , ARG A:74 , GLU F:16 , LYS F:29BINDING SITE FOR RESIDUE SO4 A1078
14BC5SOFTWAREARG C:11 , ARG D:42 , MET E:1BINDING SITE FOR RESIDUE SO4 C1078
15BC6SOFTWAREGLN C:41 , ARG C:42 , GLN C:49 , ARG C:72 , HOH C:2009 , HOH C:2010BINDING SITE FOR RESIDUE SO4 C1079

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AF4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AF4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AF4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AF4)

(-) Exons   (0, 0)

(no "Exon" information available for 5AF4)

(-) 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 .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5af4 A  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  5af4 B  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75
                                    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 .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5af4 C  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  5af4 D  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75
                                    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 .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5af4 E  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain F from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  5af4 F  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                    10        20        30        40        50        60        70    


Chain G from PDB  Type:PROTEIN  Length:73
                                                                                                        
               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
                  5af4 G  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 73
                                    10        20        30        40        50        60        70   


Chain H from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  5af4 H  1 MQIFVKTLTGRTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                    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 5AF4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AF4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AF4)

(-) Gene Ontology  (81, 83)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q96C32_HUMAN | Q96C32: 2zvn 2zvo 5af5 5af6
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

5af5 STRUCTURE OF LYS33-LINKED TRIUB S.G. P 212121
5af6 STRUCTURE OF LYS33-LINKED DIUB BOUND TO TRABID NZF1