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(-) Description

Title :  STRUCTURE OF AN UBIQUITIN COMPLEX
 
Authors :  A. Peisley, B. Wu, S. Hur
Date :  25 Nov 13  (Deposition) - 05 Mar 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Card Domain, Hydrolase-Apoptosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Peisley, B. Wu, H. Xu, Z. J. Chen, S. Hur
Structural Basis For Ubiquitin-Mediated Antiviral Signal Activation By Rig-I.
Nature V. 509 110 2014
PubMed-ID: 24590070  |  Reference-DOI: 10.1038/NATURE13140

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
    Chains: A, B, C, D
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL TANDEM CARD DOMAIN, UNP RESIDUES 1-200
    Gene: DDX58
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 58, RIG-I-LIKE RECEPTOR 1, RLR-1, RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN, RIG-1, RETINOIC ACID-INDUCIBLE GENE I PROTEIN, RIG-I
 
Molecule 2 - UBIQUITIN
    Chains: E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 76-152
    Gene: UBC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NQK)

(-) Sites  (0, 0)

(no "Site" information available for 4NQK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NQK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg D:179 -Asn D:180
2Leu H:73 -Arg H:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NQK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NQK)

(-) Exons   (0, 0)

(no "Exon" information available for 4NQK)

(-) 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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqk A   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqk B   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqk C   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqk D   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIV 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain E from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....eeee.....hhhhhhhhhhhhhh......eeee..ee......hhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 4nqk E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  72
                                    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 .eeeee.....eeeee.....hhhhhhhhhhhhhh......eeee..........hhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4nqk F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain G from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh......eeee..ee................eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4nqk G   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70 


Chain H from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh......eeee..ee................eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4nqk H   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                                    10        20        30        40        50        60        70     


Chain I from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh......eeee..ee..................eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4nqk I   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
                                    10        20        30        40        50        60        70 


Chain J from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh......eeee....................eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4nqk J   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    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 4NQK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NQK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NQK)

(-) Gene Ontology  (120, 127)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg D:179 - Asn D:180   [ RasMol ]  
    Leu H:73 - Arg H:74   [ RasMol ]  
 

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  4nqk
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  DDX58_HUMAN | O95786
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  UBC_HUMAN | P0CG48
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX58_HUMAN | O95786: 2lwd 2lwe 2qfb 2qfd 2rmj 2ykg 3lrn 3lrr 3ncu 3og8 3zd6 3zd7 4ay2 4bpb 4on9 4p4h 5e3h 5f98 5f9f 5f9h
        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 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NQK)