Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 149.02 kDa 
• Atom Count: 9,888 
• Modelled Residue Count: 1,225 
• Deposited Residue Count: 1,311 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3AVX

Structure of viral RNA polymerase complex 5

• PDB DOI:  https://doi.org/10.2210/pdb3AVX/pdb
• NDB: NA1029

• Classification: TRANSLATION, TRANSFERASE/RNA
• Organism(s): Escherichia coli O157:H7, Qubevirus durum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-08 Released: 2012-01-18 
• Deposition Author(s): Takeshita, D., Tomita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.276 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Molecular basis for RNA polymerization by Q beta replicase

Takeshita, D., Tomita, K.

(2012) Nat Struct Mol Biol 19: 229-237

• PubMed: 22245970 
• DOI: https://doi.org/10.1038/nsmb.2204
• Primary Citation of Related Structures:  
  3AVT, 3AVU, 3AVV, 3AVW, 3AVX, 3AVY


• PubMed Abstract: 
  

Core Qβ replicase comprises the Qβ virus-encoded RNA-dependent RNA polymerase (β-subunit) and the host Escherichia coli translational elongation factors EF-Tu and EF-Ts. The functions of the host proteins in the viral replicase are not clear. Structural analyses of RNA polymerization by core Qβ replicase reveal that at the initiation stage, the 3'-adenine of the template RNA provides a stable platform for de novo initiation. EF-Tu in Qβ replicase forms a template exit channel with the β-subunit. At the elongation stages, the C-terminal region of the β-subunit, assisted by EF-Tu, splits the temporarily double-stranded RNA between the template and nascent RNAs before translocation of the single-stranded template RNA into the exit channel. Therefore, EF-Tu in Qβ replicase modulates RNA elongation processes in a distinct manner from its established function in protein synthesis.

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Organizational Affiliation: 

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase	A	1,289	Escherichia coli O157:H7, Qubevirus durum	Mutation(s): 0  Gene Names: tufA EC: 2.7.7.48
UniProt
Find proteins for P14647 (Escherichia virus Qbeta) Explore P14647  Go to UniProtKB:  P14647
Find proteins for P0A6N3 (Escherichia coli O157:H7) Explore P0A6N3  Go to UniProtKB:  P0A6N3
Find proteins for P0A6P3 (Escherichia coli O157:H7) Explore P0A6P3  Go to UniProtKB:  P0A6P3
UniProt Groups	P14647P0A6P3P0A6N3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*UP*C)-3')	B [auth G]	9	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*CP*GP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3')	C [auth T]	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GH3	D [auth A]	3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 QGYIFQKZZSSUCR-OBXARNEKSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.276 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.31	α = 90
b = 256.58	β = 90
c = 101.59	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Takeshita, D., Tomita, K.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Source and taxonomy