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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BOMBYX MORI VASA HELICASE (E339Q) IN COMPLEX WITH RNA,ADP AND PI
 
Authors :  P. Spinelli, R. S. Pillai, J. Kadlec, S. Cusack
Date :  07 May 14  (Deposition) - 18 Jun 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Hydrolase, Pirna, Amplifier Complex, Transposon (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xiol, P. Spinelli, M. A. Laussmann, D. Homolka, Z. Yang, E. Cora, Y. Coute, S. Conn, J. Kadlec, R. Sachidanandam, M. Kaksonen, S. Cusack A. Ephrussi, R. S. Pillai
Rna Clamping By Vasa Assembles A Pirna Amplifier Complex On Transposon Transcripts.
Cell(Cambridge, Mass. ) V. 157 1698 2014
PubMed-ID: 24910301  |  Reference-DOI: 10.1016/J.CELL.2014.05.018

(-) Compounds

Molecule 1 - BMVLG PROTEIN
    Cell Line: BMN4 OVARIAN CELL CULTURE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: HELICASE, RESIDUES 135-564
    Mutation: YES
    Organism Common: DOMESTIC SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Synonym: BM VASA
 
Molecule 2 - 5'-R(*UP*GP*AP*CP*AP*UP)-3'
    Chains: D
    Organism Common: DOMESTIC SILKWORM
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:153 , ILE A:154 , PHE A:160 , PHE A:182 , TYR A:200 , LYS A:202 , GLN A:207 , GLN A:225 , GLY A:227 , SER A:228 , GLY A:229 , LYS A:230 , THR A:231 , ASP A:496 , ARG A:524 , VAL A:525 , PO4 A:1565 , MG A:1566 , HOH A:2005 , HOH A:2020 , HOH A:2021 , HOH A:2070BINDING SITE FOR RESIDUE ADP A1564
2AC2SOFTWARETHR A:226 , LYS A:230 , GLN A:339 , GLY A:494 , HIS A:517 , ARG A:521 , ARG A:524 , ADP A:1564 , MG A:1566 , HOH A:2038 , HOH A:2039 , HOH A:2040 , HOH A:2070BINDING SITE FOR RESIDUE PO4 A1565
3AC3SOFTWAREGLN A:339 , ADP A:1564 , PO4 A:1565 , HOH A:2021 , HOH A:2038 , HOH A:2039 , HOH A:2070BINDING SITE FOR RESIDUE MG A1566

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D26)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D26)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D26)

(-) Exons   (0, 0)

(no "Exon" information available for 4D26)

(-) 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:430
 aligned with O01378_BOMMO | O01378 from UniProtKB/TrEMBL  Length:601

    Alignment length:435
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558     
         O01378_BOMMO   129 GETKKPVTYVPPEPTNDETEIFSSTISSGINFDKFDHIAVKVSGENPPRPIESFETANLRKYVLDNVLKAGYRKPTPIQKNAIPIIMSGRDLMGCAQTGSGKTAAFLVPIINMLLQDPKDLISENGCAQPQVIIVSPTRELTLQIFNEARKFSYGSVLKVAVAYGGTAVRHQGDNIARGCHILVATPGRLHDFVERNRVSFGSVRFVVLDEADRMLDMGFMPSIEKMMLHPTMVETTKRQTLMFSATFPEDIQHLAGRFLNNYLFVAVGIVGGASTDVEQIFIEVTKYEKRNSLKQLIEENDGKRILVFVETKRNADFIAAMLSEQQLLTSSIHGDRMQREREEALQNFKSGKHCILVATAVAARGLDIKNVDIVVNYDLPKSIDEYVHRIGRTGRVGNRGKAVSFYDSDQDLALVADLSKILRQADQSVPDFLK 563
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----..........hhhhhhh.......hhhhhhhh.eeee.........hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh.....ee..ee...eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhh.....hhhhheeeeee...hhhhhhhhh......eeeee.........eeeeeee....hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeee.hhhh.........eeee.....hhhhhhhhhh........eeeeeeehhhhhh.hhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d26 A 134 G-----VTYVPPEPTNDETEIFSSTISSGINFDKFDHIAVKVSGENPPRPIESFETANLRKYVLDNVLKAGYRKPTPIQKNAIPIIMSGRDLMGCAQTGSGKTAAFLVPIINMLLQDPKDLISENGCAQPQVIIVSPTRELTLQIFNEARKFSYGSVLKVAVAYGGTAVRHQGDNIARGCHILVATPGRLHDFVERNRVSFGSVRFVVLDQADCMLDMGFMPSIEKMMLHPTMVETTKRQTLMFSATFPEDIQHLAGRFLNNYLFVAVGIVGGASTDVEQIFIEVTKYEKRNSLKQLIEENDGKRILVFVETKRNADFIAAMLSEQQLLTSSIHGDRMQREREEALQNFKSGKHCILVATAVAARGLDIKNVDIVVNYDLPKSIDEYVHRIGRTGRVGNRGKAVSFYDSDQDLALVADLSKILRQADQSVPDFLK 563
                            |     |138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558     
                            |   135                                                                                                                                                                                                                                                                                                                                                                                                                                            
                          134                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain D from PDB  Type:RNA  Length:6
                                      
                 4d26 D   1 UGACAU   6
   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 4D26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D26)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O01378_BOMMO | O01378)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  4d26
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  O01378_BOMMO | O01378
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 Related Entries

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

UniProtKB/TrEMBL
        O01378_BOMMO | O01378: 4d25

(-) Related Entries Specified in the PDB File

4d25 CRYSTAL STRUCTURE OF THE BOMBYX MORI VASA HELICASE (E339Q) IN COMPLEX WITH RNA AND AMPPNP