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(-) Description

Title :  EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE NATIVE CONFORMATION
 
Authors :  Z. Yang, K. M. Chen, R. R. Pandey, D. Homolka, M. Reuter, B. K. Rodino Jan R. Sachidanandam, M. O. Fauvarque, A. A. Mccarthy, R. S. Pillai
Date :  01 Oct 15  (Deposition) - 23 Dec 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,C,E,G,I
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  C,E  (1x)
Biol. Unit 3:  G,I  (1x)
Keywords :  Hydrolase, Exonuclease, Pirna Biogenesis, Dimer, Rna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yang, K. M. Chen, R. R. Pandey, D. Homolka, M. Reuter, B. K. Rodino Janeiro, R. Sachidanandam, M. O. Fauvarque, A. A. Mccarthy, R. S. Pillai
Piwi Slicing And Exd1 Drive Biogenesis Of Nuclear Pirnas From Cytosolic Targets Of The Mouse Pirna Pathway
Mol. Cell V. 61 138 2016
PubMed-ID: 26669262  |  Reference-DOI: 10.1016/J.MOLCEL.2015.11.009

(-) Compounds

Molecule 1 - EXD1
    Cell Line: BMN4
    Chains: A, C, E, G, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PETM-22
    Expression System Vector Type: PLASMID
    Fragment: EXONUCLEASE DOMAIN, RESIDUES 73-315
    Organ: OVARIES
    Organism Common: DOMESTIC SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ACEGI
Biological Unit 1 (2x): A    
Biological Unit 2 (1x):  CE  
Biological Unit 3 (1x):    GI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FIQ)

(-) Sites  (0, 0)

(no "Site" information available for 5FIQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:166 -Pro A:167
2Arg A:244 -Pro A:245
3Ser C:166 -Pro C:167
4Arg C:244 -Pro C:245
5Ser E:166 -Pro E:167
6Arg E:244 -Pro E:245
7Ser G:166 -Pro G:167
8Arg G:244 -Pro G:245
9Ser I:166 -Pro I:167
10Arg I:244 -Pro I:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FIQ)

(-) 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fiq A  73 KVLKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKCKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAID 314
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  


Chain C from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fiq C  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKCKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAID 314
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314


Chain E from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fiq E  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKCKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAID 314
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314


Chain G from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhh.......hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fiq G  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKCKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAID 314
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314


Chain I from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fiq I  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKCKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAID 314
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
   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 5FIQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:244 - Pro A:245   [ RasMol ]  
    Arg C:244 - Pro C:245   [ RasMol ]  
    Arg E:244 - Pro E:245   [ RasMol ]  
    Arg G:244 - Pro G:245   [ RasMol ]  
    Arg I:244 - Pro I:245   [ RasMol ]  
    Ser A:166 - Pro A:167   [ RasMol ]  
    Ser C:166 - Pro C:167   [ RasMol ]  
    Ser E:166 - Pro E:167   [ RasMol ]  
    Ser G:166 - Pro G:167   [ RasMol ]  
    Ser I:166 - Pro I:167   [ RasMol ]  
 
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  5fiq
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  EXD1_BOMMO | H9IUR0
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 Related Entries

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

UniProtKB/Swiss-Prot
        EXD1_BOMMO | H9IUR0: 5fis

(-) Related Entries Specified in the PDB File

5fis EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE GD BOUND CONFORMATION