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(-) Description

Title :  EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE GD BOUND 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 :  02 Oct 15  (Deposition) - 23 Dec 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
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
    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
 
Molecule 2 - EXD1
    Cell Line: BMN4
    Chains: B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2GD3Ligand/IonGADOLINIUM ATOM

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:138 , GLU A:266 , HOH A:2005 , HOH A:2006 , HOH A:2093 , HOH A:2094 , ASP B:113BINDING SITE FOR RESIDUE GD A1316
2AC2SOFTWAREASP A:113 , HOH A:2064 , HOH A:2065 , HOH A:2066 , ASP B:138 , GLU B:266 , HOH B:2068BINDING SITE FOR RESIDUE GD B1316
3AC3SOFTWAREGLU A:104 , HOH A:2038 , HOH A:2039 , HOH A:2040 , ASP B:314 , TYR B:315 , HOH B:2178BINDING SITE FOR RESIDUE GD A1317

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:166 -Pro A:167
2Arg A:244 -Pro A:245
3Ser B:166 -Pro B:167
4Arg B:244 -Pro B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FIS)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhh.......hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fis A  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKcKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPKKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAIDY 315
                                    84        94       104       114       124   |   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 
                                                                               128-CSO                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.eee...hhhhhhhhhhhhh..eeee......hhhhh....eeee....eeeehhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhh.......hhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fis B  75 LKISQTKYEEILKISKKYIFINQVDKSFHEAVDDLNQQDFIAVSGDGANMGRKcKMPFLVLSTDHQIYIFDIQVMQYHAFESGLKKILEGDSPRKIAHDCRKLSDCLYHKHNVKLKSVFDTQVGDLIITKNKKVTLPNKVKSLGECLTNYLGLQQNTIDEKLDIVQSTERPLSVKIKDSLARNIAFLHHLSEVINEEMQLPFYRGVECYIENIRSSDDFKAWELCGKLNQIPKEFRNAIDY 315
                                    84        94       104       114       124   |   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 
                                                                               128-CSO
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  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 5FIS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        EXD1_BOMMO | H9IUR0: 5fiq

(-) Related Entries Specified in the PDB File

5fiq EXONUCLEASE DOMAIN-CONTAINING 1 (EXD1) IN THE NATIVE CONFORMATION