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(-) Description

Title :  STRUCTURE OF AN ACTIVE LIGASE (HOIP)/UBIQUITIN TRANSFER COMPLEX
 
Authors :  R. R. Rana, B. Stieglitz, Koliopoulos M. G. , A. C. Morris-Davies, E. Christodoulou, S. Howell, N. R. Brown, K. Rittinger
Date :  05 Jul 13  (Deposition) - 16 Oct 13  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  E3 Ligase-Ubiquitin Complex, Ligase, Hoip, Rnf31, Ubiquitin, Rbr Ligase, E3 Ligase, Ring Domain, Ibr Domain, Zinc Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Stieglitz, R. R. Rana, M. G. Koliopoulos, A. C. Morris-Davies, V. Schaeffer, E. Christodoulou, S. Howell, N. R. Brown, I. Dikic, K. Rittinger
Structural Basis For Ligase-Specific Conjugation Of Linear Ubiquitin Chains By Hoip.
Nature V. 503 422 2013
PubMed-ID: 24141947  |  Reference-DOI: 10.1038/NATURE12638

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RNF31
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-49B
    Expression System Strain: BL21 GOLD
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: E3 LIGASE HOIP CATALYTIC CORE (UNP RESIDUES 853-1072)
    Gene: RNF31, ZIBRA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HOIL-1-INTERACTING PROTEIN, HOIP, RING FINGER PROTEIN 31, ZINC IN-BETWEEN-RING-FINGER UBIQUITIN-ASSOCIATED DOMAIN PROTEIN
 
Molecule 2 - POLYUBIQUITIN-C
    Chains: B
    Fragment: UNP RESIDUES 77-152
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2ZN5Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:871 , CYS A:874 , CYS A:890 , CYS A:893BINDING SITE FOR RESIDUE ZN A 1101
2AC2SOFTWARECYS A:898 , CYS A:901 , HIS A:926 , CYS A:930BINDING SITE FOR RESIDUE ZN A 1102
3AC3SOFTWARECYS A:911 , CYS A:916 , HIS A:923 , HIS A:925BINDING SITE FOR RESIDUE ZN A 1103
4AC4SOFTWARECYS A:969 , CYS A:986 , CYS A:998 , HIS A:1001BINDING SITE FOR RESIDUE ZN A 1104
5AC5SOFTWARECYS A:885 , HIS A:887 , ZN A:1106 , MET B:1 , VAL B:17 , GLU B:18 , HOH B:145BINDING SITE FOR RESIDUE IMD A 1105
6AC6SOFTWARECYS A:885 , HIS A:887 , IMD A:1105 , MET B:1BINDING SITE FOR RESIDUE ZN A 1106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:914 -Asn A:915
2Gly A:967 -Gly A:968
3Leu B:8 -Thr B:9
4Thr B:9 -Gly B:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LJO)

(-) 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:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh..eee......eee.......eee......eee......ee................ee.....hhhhhh..hhhhhhhhhhhh......................eeeeee..eeeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ljo A  857 AQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK 1072
                                   866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                             
               SCOP domains d4ljob_ B: Ubiquitin                                                         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
                4ljo B    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76
                                    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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:967 - Gly A:968   [ RasMol ]  
    Leu B:8 - Thr B:9   [ RasMol ]  
    Pro A:914 - Asn A:915   [ RasMol ]  
    Thr B:9 - Gly B:10   [ RasMol ]  
 

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  RL40_BOVIN | P63048
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  RNF31_HUMAN | Q96EP0
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 Related Entries

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

UniProtKB/Swiss-Prot
        E1B9K1_BOVIN | E1B9K1: 4ljp 4s22
        RL40_BOVIN | P63048: 1aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4ljp 4s22
        RNF31_HUMAN | Q96EP0: 2ct7 4dbg 4juy 4ljp 4ljq 4owf 4oyj 4oyk 4p09 4p0a 4p0b 5edv 5ljn

(-) Related Entries Specified in the PDB File

4ljp 4ljq