The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module. Structure 18 537-547 2010
    Site JCSG
    PDB Id 3go5 Target Id 389882
    Molecular Characteristics
    Source Streptococcus pneumoniae tigr4
    Alias Ids TPS14564,NP_345429.1, BIG_354, 85785 Molecular Weight 32417.50 Da.
    Residues 284 Isoelectric Point 5.88
    Sequence mntnlasfivgliidendrfyfvqkdgqtyalakeegqhtvgdtvkgfaytdmkqklrlttlevtatqd qfgwgrvtevrkdlgvfvdtglpdkeivvsldilpelkelwpkkgdqlyirlevdkkdriwgllayqed fqrlarpaynnmqnqnwpaivyrlklsgtfvylpennmlgfihpseryaeprlgqvldarvigfrevdr tlnlslkprsfemlendaqmiltylesnggfmtlndksspddikatfgiskgqfkkalgglmkagkikq dqfgteli
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.40 Rfree 0.175
    Matthews' coefficent 2.75 Rfactor 0.154
    Waters 668 Solvent Content 55.30

    Ligand Information


    Google Scholar output for 3go5
    1. Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module
    Y Matsumoto, Q Xu, S Miyazaki, C Kaito, CL Farr - Structure, 2010 - Elsevier

    Protein Summary

    Gene SP_0946 from Streptococcus pneumoniae tigr4 encodes the NP_345429.1 protein with four domains, likely involved in binding RNA and DNA, from the COG2996. The first three domains are tandem repeats of the S1 RNA binding domains (residues 1-63, 64-134, 135-216). The last domain (221-276) is a classic winged helix domain (WH). Both the S1 domains and WH domain display features supporting the possibility that this protein can interact with both ssRNA and dsDNA/dsRNA. Considering these properties, it is possible that NP_345429 may be involved in transcription. The primary sequence is homologous to the Staphylococcus virulence factor CvfB.

    Pre-SCOP classifies 3go5 N-terminal domains in the nucleic acid binding proteins superfamily, and the C-terminal domain in the winged helix DNA binding domain superfamily. DALI provides hits with the translation initiator factor-2 alpha PDB:1yz6 (Z=10), RNA polymerase-II PDB:2c35 (Z=9) and the MJ1198 protein PDB:2k52 (Z=9).

    Figure 1. monomer structure of 3go5


    Figure 2. Distribution of the electrostatic potential along the 3go5 structure (red: negative, blue: positive)


    Ligand Summary




    No references found.

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    Files (2)

    FileSizeDateAttached by 
    389882 monomer
    68.79 kB20:39, 5 Dec 2008qxuActions
    389882 elecstatic potential
    80.38 kB20:39, 5 Dec 2008qxuActions
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