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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MZM-REP DOMAINS OF MIND BOMB 1 IN COMPLEX WITH JAGGED1 N-BOX PEPTIDE
 
Authors :  B. J. Mcmillan, S. C. Blacklow
Date :  06 Jan 15  (Deposition) - 18 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,C
Keywords :  E3 Ligase, Notch Signaling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Mcmillan, B. Schnute, N. Ohlenhard, B. Zimmerman, L. Miles, N. Beglova, T. Klein, S. C. Blacklow
A Tail Of Two Sites: A Bipartite Mechanism For Recognition Of Notch Ligands By Mind Bomb E3 Ligases.
Mol. Cell V. 57 912 2015
PubMed-ID: 25747658  |  Reference-DOI: 10.1016/J.MOLCEL.2015.01.019

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MIB1
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MIB1, DIP1, KIAA1323, ZZANK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAPK-INTERACTING PROTEIN 1,DIP-1,MIND BOMB HOMOLOG 1,ZINC FINGER ZZ TYPE WITH ANKYRIN REPEAT DOMAIN PROTEIN 2
 
Molecule 2 - JAGGED 1 N-BOX PEPTIDE
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:85 , CYS A:88 , CYS A:109 , CYS A:112binding site for residue ZN A 501
2AC2SOFTWARECYS A:100 , CYS A:103 , HIS A:118 , HIS A:122binding site for residue ZN A 502
3AC3SOFTWAREARG A:8 , LYS A:99 , CYS A:103 , THR A:104 , ASN A:105 , ARG A:347 , HOH A:604 , HOH A:623 , HOH A:624binding site for residue SO4 A 503
4AC4SOFTWAREARG A:126 , THR A:128 , VAL A:135 , PRO A:232 , HOH A:673 , HOH A:691 , HOH A:706 , HOH A:708binding site for residue SO4 A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XI7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:91 -Pro A:92
2Ala A:314 -Ser A:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XI7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XI7)

(-) Exons   (0, 0)

(no "Exon" information available for 4XI7)

(-) 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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee................eeeeeeee..eeeeee....eeeee......eeeeehhhhh.ee............ee..eeee......eehhhhhhh........eeee.......ee..hhhhh..eeeee.....eeee................eeeeeee.........eeeeee....eeeee.hhhhh..eeeee.eeeeeehhhhh.........hhhhhhhhhh.....hhhhhhhhh...eeeee.....eeee.....eeeehhhhh..........eeee..hhhhhhhhhhhh...hhhhhhhh..eeeeeee.....eeeee..eeeeehhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xi7 A   7 SRVMVEGVGARVVRGPDWKWGKQDGGEGHVGTVRSFESPEEVVVVWDNGTAANYRCSGAYDLRILDSAPTGIKHDGTMCDTCRQQPIIGIRWKCAECTNYDLCTVCYHGDKHHLRHRFYRITTPGSERVLLESRRKSKKITARGIFAGARVVRGVDWQWEDQDGGNGRRGKVTEIQDWSASSPHSAAYVLWDNGAKNLYRVGFEGMSDLKCVQDAKGGSFYRDHCPVLGVNIDLDLEIVQSLQHGHGGWTDGMFETLTTTGTVCGIDEDHDIVVQYPSGNRWTFNPAVLTKASQFQVGDLVQVCYDLERIKLLQRGHGEWAEAMLPTLGKVGRVQQIYSDSDLKVEVCGTSWTYNPAAVSKV 400
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       252       262       272       282       292       302       312 ||    338       348       358       368       378       388       398  
                                                                                                                                                                                                                                                              235|                                                           314|                                                                     
                                                                                                                                                                                                                                                               252                                                            331                                                                     


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4xi7 C   2 QIKNPI   7
   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 4XI7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XI7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XI7)

(-) Gene Ontology  (76, 81)

Asymmetric/Biological Unit(hide GO term definitions)

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  MIB1_HUMAN | Q86YT6
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 Related Entries

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

UniProtKB/Swiss-Prot
        JAG1_HUMAN | P78504: 2kb9 2vj2 4cbz 4cc0 4cc1 5bo1
        MIB1_HUMAN | Q86YT6: 4tse 4xi6 4xib

(-) Related Entries Specified in the PDB File

4xfx 4xib