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(-) Description

Title :  DCNL COMPLEX WITH N-TERMINALLY ACETYLATED NEDD8 E2 PEPTIDE
 
Authors :  J. K. Monda, D. C. Scott, D. J. Miller, J. W. Harper, E. J. Bennett, B. A. Sc
Date :  26 Jul 12  (Deposition) - 28 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  E3 Ligase, Ligase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Monda, D. C. Scott, D. J. Miller, J. Lydeard, D. King, J. W. Harper, E. J. Bennett, B. A. Schulman
Structural Conservation Of Distinctive N-Terminal Acetylation-Dependent Interactions Across A Family Of Mammalian Nedd8 Ligation Enzymes.
Structure V. 21 42 2013
PubMed-ID: 23201271  |  Reference-DOI: 10.1016/J.STR.2012.10.013

(-) Compounds

Molecule 1 - DCN1-LIKE PROTEIN 3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DCUN1D3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DCUN1 DOMAIN-CONTAINING PROTEIN 3, DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1-LIKE PROTEIN 3
 
Molecule 2 - NEDD8-CONJUGATING ENZYME UBE2F
    Chains: F, G
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEDD8 CARRIER PROTEIN UBE2F, NEDD8 PROTEIN LIGASE UBE2F, NEDD8-CONJUGATING ENZYME 2, UBIQUITIN-CONJUGATING ENZYME E2 F
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (1x): A F 
Biological Unit 2 (1x):  B G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AME2Mod. Amino AcidN-ACETYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4GBA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:195 -Gly A:196
2Gly A:254 -Pro A:255

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GBA)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.......eehhhhhhhhhhhh.....hhhhhhhhhhh.......eehhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........eehhhhhhhhhhhh......hhhhhhhhhhhh.....eehhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gba A  89 QRLEELFRRYKDEREDAILEEGMERFCNDLCVDPTEFRVLLLAWKFQAATMCKFTRKEFFDGCKAISADSIDGICARFPSLLTEAKQEDKFKDLYRFTFQFGLDSEEGQRSLHREIAIALWKLVFTQNNPPVLDQWLNFLTENPSGIKGISRDTWNMFLNFTQVIGPDLSNYSEDEAWPSLFDTFVEWEMERRKRE 284
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....eehhhhhhhhhhhhh....hhhhhhhhhhh.......eehhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhh......hhhhhhhhhhhh......eehhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gba B  89 QRLEELFRRYKDEREDAILEEGMERFCNDLCVDPTEFRVLLLAWKFQAATMCKFTRKEFFDGCKAISADSIDGICARFPSLLTEAKQEDKFKDLYRFTFQFGLDSEEGQRSLHREIAIALWKLVFTQNNPPVLDQWLNFLTENPSGIKGISRDTWNMFLNFTQVIGPDLSNYSEDEAWPSLFDTFVEWEMERRKREGEGRGALSSG 294
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288      


Chain F from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4gba F   1 xLTLASKLK   9
                            |        
                            1-AME    


Chain G from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4gba G   1 xLTLASKLK   9
                            |        
                            1-AME
   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 4GBA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 26)

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  Cis Peptide Bonds
    Glu A:195 - Gly A:196   [ RasMol ]  
    Gly A:254 - Pro A:255   [ RasMol ]  
 
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 Related Entries

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        UBE2F_HUMAN | Q969M7: 2edi 3fn1

(-) Related Entries Specified in the PDB File

4gao