4Q7J

Complex structure of viral RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 

wwPDB Validation 3D Report Full Report



Literature

Molecular insights into replication initiation by Q beta replicase using ribosomal protein S1

Takeshita, D.Yamashita, S.Tomita, K.

(2014) Nucleic Acids Res 

  • DOI: 10.1093/nar/gku745
  • Primary Citation of Related Structures:  
    4Q7J

  • PubMed Abstract: 
  • Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Qβ replicase, together with ...

    Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Qβ replicase, together with EF-Tu and EF-Ts, for Qβ RNA replication in E. coli. We analyzed the crystal structure of Qβ replicase, consisting of the virus-encoded RNA-dependent RNA polymerase (β-subunit), EF-Tu, EF-Ts and the N-terminal half of S1, which is capable of initiating Qβ RNA replication. Structural and biochemical studies revealed that the two N-terminal OB-folds of S1 anchor S1 onto the β-subunit, and the third OB-fold is mobile and protrudes beyond the surface of the β-subunit. The third OB-fold mainly interacts with a specific RNA fragment derived from the internal region of Qβ RNA, and its RNA-binding ability is required for replication initiation of Qβ RNA. Thus, the third mobile OB-fold of S1, which is spatially anchored near the surface of the β-subunit, primarily recruits the Qβ RNA toward the β-subunit, leading to the specific and efficient replication initiation of Qβ RNA, and S1 functions as a replication initiation factor, beyond its established function in protein synthesis.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan kozo-tomita@aist.go.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor TsA, E282Escherichia coli K-12Mutation(s): 0 
Gene Names: tsfb0170JW0165
Find proteins for P0A6P1 (Escherichia coli (strain K12))
Explore P0A6P1 
Go to UniProtKB:  P0A6P1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Tu 1B, F393Escherichia coli K-12Mutation(s): 0 
Gene Names: tufAb3339JW3301
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Q beta replicaseC, G594Escherichia virus QbetaMutation(s): 0 
EC: 2.7.7.48
Find proteins for P14647 (Escherichia phage Qbeta)
Explore P14647 
Go to UniProtKB:  P14647
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S1D, H281Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsAssyFb0911JW0894
Find proteins for P0AG67 (Escherichia coli (strain K12))
Explore P0AG67 
Go to UniProtKB:  P0AG67
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
C, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.19α = 90
b = 150.83β = 90
c = 189.78γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-04-25 
  • Released Date: 2014-08-27 
  • Deposition Author(s): Takeshita, D.

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release